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Alternate allele filtering?
I am trying to call Het as: Ref allele 10-90% or Alt allele 10-90. I have four samples. If one sample is Het, that location is preserved if criteria for Het (as earlier) and Homozygous (> 90% of Alt or Ref allele) at other three locations are met. Is there any simple way to achieve this?
I was just trying SelectVariants to filter with these criteria and tried to see if things works. I used <5% alternate allele for first sample and still can see locations with > 5% alt allele. Here are the code and output. please let me know if I am doing wrong? Thanks
$java -jar $gatk -T SelectVariants -R 8771mapped_Pcap_211contigs.fasta -V snps_after_hardFilter_20x.vcf -o snps_after_hardFilter_20x_alt10_allHet.vcf -select 'vc.getGenotype("7290_R1").getAD().1 / vc.getGenotype("7290_R1").getDP() < 0.05'
I got alt allele of 23/92 = 0.25
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 7290_R1 7291_R1 8566_R1 8771_R1 2 2212 . G A 592.90 PASSS AC=2;AF=0.250;AN=8;BaseQRankSum=0.845;ClippingRankSum=0.000;DP=257;ExcessHet=3.6798;FS=0.000;ML EAC=2;MLEAF=0.250;MQ=60.00;MQRankSum=0.000;QD=4.94;ReadPosRankSum=-2.023;SOR=0.687 GT:AD:DP:GQ:PL 0/1:69,23:92:99:518,0,2196 0/1:21,7:28:99:109,0,533 0/0:43,0:43:99:0,129,1439 0/0:91,2:93:99:0,223,2719