pGoM.sh filtering

[speleonut]

1. For generalising the script you may not be able to enforce which order child, mother and father are placed in the VCF or if there are other samples etc. It would be better to use your initial SAMPLELIST file that gets fed to the master script, extract the ID from that and explicitly map their column number in the VCF e.g. a solution like this: https://unix.stackexchange.com/questions/524186/column-number-of-matching-string-in-column might do it.
2. The script will not pick up phased variants based on the search patterns used e.g. 0/1 alleles but not 0|1 or 1|0 alleles which Mutect2 might produce.

[ngs1810]

1. Thanks for the reference.. I guess i wasnt able to define my variables in awk command previously, so i just stick to the order. However, i have amended the script now. It could be simplified further but Let me know what you think the latest one (pGoM.sh).