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I have selected those variants that are covered in my 7 samples (diploid organism) with AN=14 and then I applied the VariantFiltration walker in order to filter those that have less than 6X of coverage.
Keep variants with AN=14 (7 samples / diploid organism = 7*2=14)
java -jar GenomeAnalysisTK.jar -T SelectVariants -R sequence.fasta -select "AN==14" --variant cohort.vcf -o cohort.AN.vcf
Mark variants having DP<6
java -jar GenomeAnalysisTK.jar -T VariantFiltration -R sequence.fasta --genotypeFilterExpression "DP<6" --genotypeFilterName LowDP --variant cohort.AN.vcf -o cohort.AN.DP.vcf
Remove LowDP marked variants
grep -vw "LowDP" cohort.AN.DP.vcf > cohort.filtered.vcf
But when I check this I see that in some variants my lowDP filter is not working, for example:
GL622784 1350823 . C T 8109.01 PASS AC=13;AF=0.929;AN=14;BaseQRankSum=-1.369e+00;ClippingRankSum=1.79;DP=176;FS=1.661;MLEAC=13;MLEAF=0.929;MQ=58.94;MQRankSum=2.78;QD=33.65;ReadPosRankSum=0.678;SOR=0.307 GT:AD:DP:GQ:PL
1/1:0,48:48:99:1|1:1350822_T_C:2247,156,0 1/1:0,22:22:72:1|1:1350797_C_T:1069,72,0 1/1:0,0:.:6:1|1:1350822_T_C:49,6,0
1/1:0,17:17:51:1|1:1350797_C_T:765,51,0 1/1:0,14:14:42:1|1:1350822_T_C:630,42,0 0/1:6,7:13:99:0|1:1350822_T_C:276,0,231
Am I missing something here? I thought this should work.
Any hint on this will be very helpful
Thanks a lot!