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bcftools 1.21 merge gvcfs results in more than one variant at the same location for complex polyallelic MNP variants, continuation of #2333 #2356

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jcm6t opened this issue Jan 21, 2025 · 0 comments
Open

bcftools 1.21 merge gvcfs results in more than one variant at the same location for complex polyallelic MNP variants, continuation of #2333 #2356

jcm6t opened this issue Jan 21, 2025 · 0 comments

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@jcm6t
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jcm6t commented Jan 21, 2025

Referencing the closed #2333. I cannot reopen that issue.

Tested the changed 1.21 version including commit 7427402

bcftools 1.21-68-g0d635700-dirty
Using htslib 1.21-20-gc705bec2-dirty

Ran chromosome 1 using the same pipeline as #2333
While the changes in the commit certainly fixed the specific test case exemplified in #2333 there are still many duplicate variants in the data.

$BCFTOOLS view -H -r chr14:53952388 PRECIS_all_chr14.bcf | cut -f1-8
chr14	53952387	.	CA	C	39.13	PASS	MQRankSum=4.805;ReadPosRankSum=1.526;FractionInformativeReads=0.941;DP=65;DQUAL=50;MQ=250
chr14	53952388	.	A	C	59.97	PASS	MQRankSum=4.002;ReadPosRankSum=1.98;FractionInformativeReads=1;DP=32296;DQUAL=11.67;MQ=247.47

Define a duplicate variant in the output vcf file generated from the input gvcfs as identical CHR, POS, REF, ALT.
In the chr 1 file there were 464,424 duplicate variants in the chr 1 output from 1379 WGCV gvcfs. There are clearly still fundamental problem(s) in merge/norm gvcfs, and I believe these are linked to complex MNP regions.

Here are 2 examples:

$BCFTOOLS view -H -r chr1:233339377 PRECIS_all_chr1.bcf | cut -f1-8
chr1	233339374	.	CCTTCTT	TCTTCTT	35.7	PASS	MQRankSum=2.196;ReadPosRankSum=-1.083;FractionInformativeReads=0.75;DP=32;DQUAL=50;MQ=167.83
chr1	233339374	.	CCTTCTT	C	24.76	PASS	MQRankSum=-3.298;ReadPosRankSum=-2.372;FractionInformativeReads=0.469;DP=295;DQUAL=21.08;MQ=166.79
chr1	233339377	.	T	C	27.75	PASS	MQRankSum=0.935;ReadPosRankSum=1.203;FractionInformativeReads=0.382;DP=337;DQUAL=26.31;MQ=180.414
chr1	233339377	.	T	C	26.07	PASS	FractionInformativeReads=0.5;DP=141;DQUAL=29.32;MQ=157.78
chr1	233339377	.	T	TCCTC	26.07	PASS	FractionInformativeReads=0.5;DP=141;DQUAL=29.32;MQ=157.78
chr1	233339377	.	T	TCCTC	25.27	PASS	MQRankSum=-3.682;ReadPosRankSum=-1.004;FractionInformativeReads=0.65;DP=309;DQUAL=24.86;MQ=161.228
chr1	233339377	.	TCTTCTC	T	40.29	PASS	MQRankSum=2.751;ReadPosRankSum=-2.128;FractionInformativeReads=0.897;DP=252;DQUAL=43.28;MQ=186.91
chr1	233339377	.	TCTTCTC	T	18.59	PASS	FractionInformativeReads=0.519;DP=27;DQUAL=128.75;MQ=179.6
chr1	233339377	.	TCTTCTC	TCCTCCTTCTC	18.59	PASS	FractionInformativeReads=0.519;DP=27;DQUAL=128.75;MQ=179.6

and

$BCFTOOLS view -H -r chr1:190840844 PRECIS_all_chr1.bcf | cut -f1-8
chr1	190840844	.	G	GTTTTTTTTTTTTTTTT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GTTTTTTTTTTTT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GTTTTTTTTTTTTTT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GTTTTTTTTTTTTT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTT	25.03	PASS	FractionInformativeReads=0.286;MQRankSum=0.25;ReadPosRankSum=-0.083;DP=770;DQUAL=26.26;MQ=215.85
chr1	190840844	.	G	GTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTGTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTGTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTGTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTT	39.65	PASS	MQRankSum=0.234;ReadPosRankSum=0.983;FractionInformativeReads=0.857;DP=10817;DQUAL=12.06;MQ=213.805
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTGTTTTTTTTTT	36.26	PASS	FractionInformativeReads=0.353;MQRankSum=-0.307;ReadPosRankSum=-0.482;DP=2795;DQUAL=31.33;MQ=213.203
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTT	33.01	PASS	MQRankSum=1.422;ReadPosRankSum=1.422;FractionInformativeReads=0.75;DP=1604;DQUAL=25.44;MQ=214.29
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTT	26.26	PASS	FractionInformativeReads=0.185;MQRankSum=0.474;ReadPosRankSum=1.107;DP=967;DQUAL=21.51;MQ=211.472
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTT	27.07	PASS	FractionInformativeReads=0.55;MQRankSum=0.794;ReadPosRankSum=1.66;DP=768;DQUAL=23.54;MQ=217.625
chr1	190840844	.	G	GTTTTTTTTTTTTT	27.07	PASS	FractionInformativeReads=0.55;MQRankSum=0.794;ReadPosRankSum=1.66;DP=768;DQUAL=23.54;MQ=217.625
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	27.07	PASS	FractionInformativeReads=0.55;MQRankSum=0.794;ReadPosRankSum=1.66;DP=768;DQUAL=23.54;MQ=217.625
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTT	27.07	PASS	FractionInformativeReads=0.55;MQRankSum=0.794;ReadPosRankSum=1.66;DP=768;DQUAL=23.54;MQ=217.625
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	27.07	PASS	FractionInformativeReads=0.55;MQRankSum=0.794;ReadPosRankSum=1.66;DP=768;DQUAL=23.54;MQ=217.625
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTT	27.07	PASS	FractionInformativeReads=0.55;MQRankSum=0.794;ReadPosRankSum=1.66;DP=768;DQUAL=23.54;MQ=217.625
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	27.07	PASS	FractionInformativeReads=0.55;MQRankSum=0.794;ReadPosRankSum=1.66;DP=768;DQUAL=23.54;MQ=217.625
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTT	27.07	PASS	FractionInformativeReads=0.55;MQRankSum=0.794;ReadPosRankSum=1.66;DP=768;DQUAL=23.54;MQ=217.625
chr1	190840844	.	G	GTTTTTTTTTTTTTTT	27.07	PASS	FractionInformativeReads=0.55;MQRankSum=0.794;ReadPosRankSum=1.66;DP=768;DQUAL=23.54;MQ=217.625
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTT	27.07	PASS	FractionInformativeReads=0.55;MQRankSum=0.794;ReadPosRankSum=1.66;DP=768;DQUAL=23.54;MQ=217.625
chr1	190840844	.	G	GT	27.07	PASS	FractionInformativeReads=0.55;MQRankSum=0.794;ReadPosRankSum=1.66;DP=768;DQUAL=23.54;MQ=217.625
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	38.94	PASS	FractionInformativeReads=0.5;MQRankSum=1.991;ReadPosRankSum=-0.83;DP=720;DQUAL=23.12;MQ=217.3
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	38.94	PASS	FractionInformativeReads=0.5;MQRankSum=1.991;ReadPosRankSum=-0.83;DP=720;DQUAL=23.12;MQ=217.3
chr1	190840844	.	G	GT	38.94	PASS	FractionInformativeReads=0.5;MQRankSum=1.991;ReadPosRankSum=-0.83;DP=720;DQUAL=23.12;MQ=217.3
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTT	38.94	PASS	FractionInformativeReads=0.5;MQRankSum=1.991;ReadPosRankSum=-0.83;DP=720;DQUAL=23.12;MQ=217.3
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTT	27.3	PASS	MQRankSum=1.528;ReadPosRankSum=-0.231;FractionInformativeReads=0.731;DP=429;DQUAL=36.64;MQ=211.495
chr1	190840844	.	G	GTTTTTTTTTTTTT	27.3	PASS	MQRankSum=1.528;ReadPosRankSum=-0.231;FractionInformativeReads=0.731;DP=429;DQUAL=36.64;MQ=211.495
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTT	27.3	PASS	MQRankSum=1.528;ReadPosRankSum=-0.231;FractionInformativeReads=0.731;DP=429;DQUAL=36.64;MQ=211.495
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	27.3	PASS	MQRankSum=1.528;ReadPosRankSum=-0.231;FractionInformativeReads=0.731;DP=429;DQUAL=36.64;MQ=211.495
chr1	190840844	.	G	GTTTTTTTTTTTTTTT	27.3	PASS	MQRankSum=1.528;ReadPosRankSum=-0.231;FractionInformativeReads=0.731;DP=429;DQUAL=36.64;MQ=211.495
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTT	29.18	PASS	FractionInformativeReads=0.286;MQRankSum=0.619;ReadPosRankSum=-2.023;DP=369;DQUAL=34.4;MQ=220.263
chr1	190840844	.	G	GTTTTTTTTTTTTT	29.18	PASS	FractionInformativeReads=0.286;MQRankSum=0.619;ReadPosRankSum=-2.023;DP=369;DQUAL=34.4;MQ=220.263
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	29.18	PASS	FractionInformativeReads=0.286;MQRankSum=0.619;ReadPosRankSum=-2.023;DP=369;DQUAL=34.4;MQ=220.263
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTT	29.18	PASS	FractionInformativeReads=0.286;MQRankSum=0.619;ReadPosRankSum=-2.023;DP=369;DQUAL=34.4;MQ=220.263
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTT	29.18	PASS	FractionInformativeReads=0.286;MQRankSum=0.619;ReadPosRankSum=-2.023;DP=369;DQUAL=34.4;MQ=220.263
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	29.18	PASS	FractionInformativeReads=0.286;MQRankSum=0.619;ReadPosRankSum=-2.023;DP=369;DQUAL=34.4;MQ=220.263
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	29.18	PASS	FractionInformativeReads=0.286;MQRankSum=0.619;ReadPosRankSum=-2.023;DP=369;DQUAL=34.4;MQ=220.263
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	29.18	PASS	FractionInformativeReads=0.286;MQRankSum=0.619;ReadPosRankSum=-2.023;DP=369;DQUAL=34.4;MQ=220.263
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	22.48	PASS	FractionInformativeReads=0.333;MQRankSum=0.849;ReadPosRankSum=-1.262;DP=230;DQUAL=34.83;MQ=223.62
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	22.48	PASS	FractionInformativeReads=0.333;MQRankSum=0.849;ReadPosRankSum=-1.262;DP=230;DQUAL=34.83;MQ=223.62
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTT	22.48	PASS	FractionInformativeReads=0.333;MQRankSum=0.849;ReadPosRankSum=-1.262;DP=230;DQUAL=34.83;MQ=223.62
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTT	22.48	PASS	FractionInformativeReads=0.333;MQRankSum=0.849;ReadPosRankSum=-1.262;DP=230;DQUAL=34.83;MQ=223.62
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTT	19.88	PASS	MQRankSum=3.076;ReadPosRankSum=0.927;FractionInformativeReads=0.862;DP=220;DQUAL=24.79;MQ=214.48
chr1	190840844	.	G	GTTTTTTTTTTTTT	19.88	PASS	MQRankSum=3.076;ReadPosRankSum=0.927;FractionInformativeReads=0.862;DP=220;DQUAL=24.79;MQ=214.48
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	19.88	PASS	MQRankSum=3.076;ReadPosRankSum=0.927;FractionInformativeReads=0.862;DP=220;DQUAL=24.79;MQ=214.48
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	19.88	PASS	MQRankSum=3.076;ReadPosRankSum=0.927;FractionInformativeReads=0.862;DP=220;DQUAL=24.79;MQ=214.48
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	19.88	PASS	MQRankSum=3.076;ReadPosRankSum=0.927;FractionInformativeReads=0.862;DP=220;DQUAL=24.79;MQ=214.48
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	19.88	PASS	MQRankSum=3.076;ReadPosRankSum=0.927;FractionInformativeReads=0.862;DP=220;DQUAL=24.79;MQ=214.48
chr1	190840844	.	G	GTTTTTTTTTTTT	22.72	PASS	MQRankSum=0.31;ReadPosRankSum=-1.094;FractionInformativeReads=0.816;DP=162;DQUAL=39.73;MQ=209.113
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTT	22.72	PASS	MQRankSum=0.31;ReadPosRankSum=-1.094;FractionInformativeReads=0.816;DP=162;DQUAL=39.73;MQ=209.113
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	21.53	PASS	FractionInformativeReads=0.69;MQRankSum=0.8;ReadPosRankSum=-0.667;DP=62;DQUAL=28.1;MQ=216.067
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	21.53	PASS	FractionInformativeReads=0.69;MQRankSum=0.8;ReadPosRankSum=-0.667;DP=62;DQUAL=28.1;MQ=216.067
chr1	190840844	.	G	GTTTTTTTTTTTTTTTT	7.78	PASS	MQRankSum=3.618;ReadPosRankSum=-1.007;FractionInformativeReads=0.75;DP=28;DQUAL=24.34;MQ=225.5
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTT	21.46	PASS	MQRankSum=0.794;ReadPosRankSum=-0.072;FractionInformativeReads=0.556;DP=182;DQUAL=26.01;MQ=219.618
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTT	21.46	PASS	MQRankSum=0.794;ReadPosRankSum=-0.072;FractionInformativeReads=0.556;DP=182;DQUAL=26.01;MQ=219.618
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTT	16.35	PASS	FractionInformativeReads=0.625;DP=76;DQUAL=30.06;MQ=217.587
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTT	16.35	PASS	FractionInformativeReads=0.625;DP=76;DQUAL=30.06;MQ=217.587
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTT	16.35	PASS	FractionInformativeReads=0.625;DP=76;DQUAL=30.06;MQ=217.587
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTT	23.64	PASS	FractionInformativeReads=0.55;DP=67;DQUAL=47.26;MQ=219.433
chr1	190840844	.	G	GTTTTTTTTTTTTTTT	23.64	PASS	FractionInformativeReads=0.55;DP=67;DQUAL=47.26;MQ=219.433
chr1	190840844	.	G	GT	35.57	PASS	FractionInformativeReads=0.767;DP=30;DQUAL=166.71;MQ=218.99
chr1	190840844	.	G	GTTTTTTTT	25.41	PASS	MQRankSum=0.735;ReadPosRankSum=0.105;FractionInformativeReads=0.742;DP=204;DQUAL=36.42;MQ=206.481
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTT	26.08	PASS	FractionInformativeReads=0.556;MQRankSum=2.666;ReadPosRankSum=-0.759;DP=146;DQUAL=44.88;MQ=217.08
chr1	190840844	.	G	GTTTTTTTTTTTTT	26.08	PASS	FractionInformativeReads=0.556;MQRankSum=2.666;ReadPosRankSum=-0.759;DP=146;DQUAL=44.88;MQ=217.08
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTT	15.58	PASS	MQRankSum=2.739;ReadPosRankSum=-1.659;FractionInformativeReads=0.8;DP=39;DQUAL=48.95;MQ=224.735
chr1	190840844	.	G	GTTTTTTTTTTTTT	27.73	PASS	MQRankSum=0.394;ReadPosRankSum=-0.197;FractionInformativeReads=0.75;DP=109;DQUAL=41.86;MQ=215.77
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	21.56	PASS	MQRankSum=1.2;ReadPosRankSum=-1.493;FractionInformativeReads=0.8;DP=123;DQUAL=22.03;MQ=214.647
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	21.56	PASS	MQRankSum=1.2;ReadPosRankSum=-1.493;FractionInformativeReads=0.8;DP=123;DQUAL=22.03;MQ=214.647
chr1	190840844	.	G	GTTTTTTGTTTTTTT	10.61	PASS	MQRankSum=-0.039;ReadPosRankSum=-1.362;FractionInformativeReads=0.875;DP=44;DQUAL=43.3;MQ=227.285
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	10.61	PASS	MQRankSum=-0.039;ReadPosRankSum=-1.362;FractionInformativeReads=0.875;DP=44;DQUAL=43.3;MQ=227.285
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTT	14.11	PASS	MQRankSum=-0.065;ReadPosRankSum=-1.485;FractionInformativeReads=0.667;DP=48;DQUAL=37.44;MQ=210.155
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	13.23	PASS	MQRankSum=0.206;ReadPosRankSum=-1.196;FractionInformativeReads=0.833;DP=51;DQUAL=38.03;MQ=224.895
chr1	190840844	.	G	GTT	24.43	PASS	MQRankSum=-1.313;ReadPosRankSum=-1.182;FractionInformativeReads=0.71;DP=31;DQUAL=50;MQ=213.34
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	11.97	PASS	MQRankSum=1.294;ReadPosRankSum=0.925;FractionInformativeReads=0.545;DP=43;DQUAL=32.81;MQ=229.79
chr1	190840844	.	G	GTTTTTTTTTTTTTTTTTTTTTTT	16.96	PASS	FractionInformativeReads=0.381;DP=21;DQUAL=75.73;MQ=227.09

Test case will be delivered per previously when you are ready to look this.
Thanks for your support.
Joe.
@jcm6t jcm6t changed the title bcftools 1.20 merge gvcfs results in more than one variant at the same location for complex polyallelic MNP variants, continuation of #2333 bcftools 1.21 merge gvcfs results in more than one variant at the same location for complex polyallelic MNP variants, continuation of #2333 Jan 21, 2025
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