Does not see all variants with REF allele longer than 1 letter

[Reba13]

Was running many samples, all variants with REF allele longer than A, T, C or G were without any interpretation (so all deletions were missing).
What is interesting, with ALT allele longer than one letter everything works correctly.

Was using .avinput format
Is there any ways to fix it?
Thank you in advance.

Example:

#Chr	Start	End	Ref	Alt	Ref.Gene	Func.refGene	ExonicFunc.refGene	Gene.ensGene	avsnp147	AAChange.ensGene	AAChange.refGene	clinvar: Clinvar	InterVar: InterVar and Evidence	Freq_gnomAD_genome_ALL	Freq_esp6500siv2_all	Freq_1000g2015aug_all	CADD_raw	CADD_phred	SIFT_score	GERP++_RS	phyloP46way_placental	dbscSNV_ADA_SCORE	dbscSNV_RF_SCORE	Interpro_domain	AAChange.knownGene	rmsk	MetaSVM_score	Freq_gnomAD_genome_POPs	OMIM	Phenotype_MIM	OrphaNumber	Orpha
1	985443	985443	AG	A	.	.	.	.	.	.	.	clinvar: UNK	InterVar: Uncertain significance PVS1=0 PS=[0, 0, 0, 0, 0] PM=[0, 1, 0, 0, 0, 0, 0] PP=[0, 0, 0, 0, 0, 0] BA1=0 BS=[0, 0, 0, 0, 0] BP=[0, 0, 0, 0, 0, 0, 0, 0]	.	.	.	.	.	.	.	.	.	.	.	.	.	.	AFR:.,AMR:.,EAS:.,FIN:.,NFE:.,OTH:.,ASJ:.	.	.

#Chr	Start	End	Ref	Alt	Ref.Gene	Func.refGene	ExonicFunc.refGene	Gene.ensGene	avsnp147	AAChange.ensGene	AAChange.refGene	clinvar: Clinvar	InterVar: InterVar and Evidence	Freq_gnomAD_genome_ALL	Freq_esp6500siv2_all	Freq_1000g2015aug_all	CADD_raw	CADD_phred	SIFT_score	GERP++_RS	phyloP46way_placental	dbscSNV_ADA_SCORE	dbscSNV_RF_SCORE	Interpro_domain	AAChange.knownGene	rmsk	MetaSVM_score	Freq_gnomAD_genome_POPs	OMIM	Phenotype_MIM	OrphaNumber	Orpha
1	664487	664487	AG	-	.	.	.	.	.	.	.	clinvar: UNK	InterVar: Uncertain significance PVS1=0 PS=[0, 0, 0, 0, 0] PM=[0, 1, 0, 0, 0, 0, 0] PP=[0, 0, 0, 0, 0, 0] BA1=0 BS=[0, 0, 0, 0, 0] BP=[0, 0, 0, 0, 0, 0, 0, 0]	.	.	.	.	.	.	.	.	.	.	.	.	.	.	AFR:.,AMR:.,EAS:.,FIN:.,NFE:.,OTH:.,ASJ:.	.	.

[quanliustc]

How you prepared the avinput? were you using vcf file? The avinput of these two variants, should be as:
1 985444 985444 G -
1 664487 664488 AG -
if you not sure avinput format, then do suggest you start from vcf format.

[Reba13]

I prepared avinput format extracting chr pos and ref/alt alleles information from VCF file (using awk)
If I run InterVar using VCF file as input it is removing 3/4 of all variants.

[quanliustc]

for SNV, you can directly get the avinput with ref /alt and position, but for deletions, need some change, so please read the manual of avinput at here: https://www.openbioinformatics.org/annovar/annovar_input.html

[kaichop]

Please use VCF file for variant interpretation. You cannot just use awk to generate an avinput file from VCF file, it is wrong. I am not sure what you meant by "removing 3/4 of all variants". The output should have the same number of variants from input, if there is indeed a variant with 0/1 or 1/1 genotype in the VCF file.

…

On Sat, Jul 9, 2022 at 9:31 AM Quan LI ***@***.***> wrote: for SNV, you can directly get the avinput with ref /alt and position, but for deletions, need some change, so please read the manual of avinput at here: https://www.openbioinformatics.org/annovar/annovar_input.html — Reply to this email directly, view it on GitHub <#83 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OD2TSCCSHZ4FCGOZADVTF5M3ANCNFSM53DC5T4Q> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Reba13]

Thank you so much, I will try to fix it