hi
I am new for tools such as samtools, bcftools, BWA and GATK and I am working on RADSeq I reach for point call variants which include ( INDEL and SNP) now time to filter them I could not do that by GATK with VQSR which reuired resources bundle folder which are not available for my organisms plant ( 5 samples for Cardamine hirsuta and 197 samples for Arabidopsis thaliana ) so only can do Hard-filtering however I need to plot my data to see my original distribution so I can determine thresholds which need to be filtered by considering lower est thresholds ... so I need to grep only INFO col first then how to select DP ,VDB ;AF1;MQ and so one so I can obtain file for each one which will be easier to plot then in R ...
Thanks in advance
