Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Variant filtration by allelic balance bias

mpmachadompmachado LisboaMember

Hi everyone,

I'm trying to find a way to filter some heterozygous genotypes that might have been misassigned due to PCR or sequencing errors and result in a very unrealistic allelic balance bias like the following (bias greater than 1/3 or sometimes greater than 1/4):

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RCS12
6 26088662 . T G 21188.57 PASS AC=24;AF=0.480;AN=50;AS_BaseQRankSum=-3.650;AS_FS=6.798;AS_InbreedingCoeff=-0.0015;AS_MQ=43.72;AS_MQRankSum=-0.700;AS_QD=14.87;AS_ReadPosRankSum=-0.050;AS_SOR=0.588;BaseQRankSum=-2.573e+00;DP=1845;ExcessHet=2.7216;FS=6.798;InbreedingCoeff=-0.0015;MLEAC=25;MLEAF=0.481;MQ=43.75;MQRankSum=-6.640e-01;NDA=1;QD=14.87;ReadPosRankSum=-1.400e-02;SOR=0.588 GT:AD:DP:FT:GQ:PL 0/1:5,20:25:PASS:74:418,0,74
6 26090224 . T C 8949.70 PASS AC=15;AF=0.288;AN=52;AS_BaseQRankSum=-2.300;AS_FS=1.761;AS_InbreedingCoeff=0.1568;AS_MQ=38.03;AS_MQRankSum=-0.800;AS_QD=12.24;AS_ReadPosRankSum=0.600;AS_SOR=0.547;BaseQRankSum=-1.452e+00;DP=1588;ExcessHet=0.9921;FS=1.761;InbreedingCoeff=0.1568;MLEAC=15;MLEAF=0.288;MQ=38.52;MQRankSum=-6.890e-01;NDA=1;QD=12.24;ReadPosRankSum=0.345;SOR=0.547 GT:AD:DP:GQ:PL 0/1:17,4:21:48:48,0,432
6 26090951 . C G 6430.41 PASS AC=7;AF=0.135;AN=52;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_InbreedingCoeff=-0.1556;AS_MQ=43.86;AS_MQRankSum=-0.500;AS_QD=10.31;AS_ReadPosRankSum=1.700;AS_SOR=0.637;BaseQRankSum=0.221;DP=1697;ExcessHet=5.0213;FS=0.000;InbreedingCoeff=-0.1556;MLEAC=7;MLEAF=0.135;MQ=43.85;MQRankSum=-4.380e-01;NDA=1;QD=10.31;ReadPosRankSum=-1.650e-01;SOR=0.637 GT:AD:DP:GQ:PL 0/1:9,37:46:99:918,0,140

I found that, in the past, GATK had the AlleleBalanceBySample annotation that would be very useful to remove the genotype assigned in such situations.
I know that I can do that using JEXL expressions sample by sample. However, when genotyping several samples together, iterating over the samples it's time consuming.

Do you know a faster way of doing such thing?

Thank you in advance.

Best regards,

Miguel

Answers

Sign In or Register to comment.