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Read depth and allele depth is low / zero #2168

Closed irbinveliz closed 2 months ago

irbinveliz commented 2 months ago

Hi, I have called variants using bcftools 1.17. These were the commands: bcftools mpileup --threads 20 -Ou -Q 30 -q 30 -C 50 -a AD,DP -f $reference -R $UCE_forward $input | bcftools call --threads 20 -c -Ob > $variant

However, when I look at the bcf file, there are many positions for which the AD and DP is zero. I would say that also the PL looks strange.

NC_000001.11    90067536        .       A       .       38.9945 .       DP=3;MQ0F=0;AF1=0;AC1=0;DP4=0,3,0,0;MQ=37;FQ=-35.9869 GT:PL:DP:AD     0/0:0:3:3
NC_000001.11    90067537        .       T       .       38.9945 .       DP=3;MQ0F=0;AF1=0;AC1=0;DP4=0,3,0,0;MQ=37;FQ=-35.9869 GT:PL:DP:AD     0/0:0:3:3
NC_000001.11    90067538        .       C       .       35.995  .       DP=3;MQ0F=0;AF1=0;AC1=0;DP4=0,2,0,0;MQ=39;FQ=-32.988  GT:PL:DP:AD     0/0:0:2:2
NC_000001.11    90067539        .       T       .       38.9945 .       DP=3;MQ0F=0;AF1=0;AC1=0;DP4=0,3,0,0;MQ=37;FQ=-35.9869 GT:PL:DP:AD     0/0:0:3:3
NC_000001.11    90067540        .       T       .       38.9945 .       DP=3;MQ0F=0;AF1=0;AC1=0;DP4=0,3,0,0;MQ=37;FQ=-35.9869 GT:PL:DP:AD     0/0:0:3:3
NC_000001.11    90067541        .       T       .       38.9945 .       DP=3;MQ0F=0;AF1=0;AC1=0;DP4=0,3,0,0;MQ=37;FQ=-35.9869 GT:PL:DP:AD     0/0:0:3:3
NC_000001.11    90067542        .       A       .       38.9945 .       DP=3;MQ0F=0;AF1=0;AC1=0;DP4=0,3,0,0;MQ=37;FQ=-35.9869 GT:PL:DP:AD     0/0:0:3:3
NC_000001.11    90067543        .       A       .       35.995  .       DP=2;MQ0F=0;AF1=0;AC1=0;DP4=0,2,0,0;MQ=37;FQ=-32.988  GT:PL:DP:AD     0/0:0:2:2
NC_000001.11    90067544        .       C       .       35.995  .       DP=2;MQ0F=0;AF1=0;AC1=0;DP4=0,2,0,0;MQ=37;FQ=-32.988  GT:PL:DP:AD     0/0:0:2:2
NC_000001.11    90067545        .       A       .       32.9944 .       DP=1;MQ0F=0;AF1=0;AC1=0;DP4=0,1,0,0;MQ=34;FQ=-29.9918 GT:PL:DP:AD     0/0:0:1:1
NC_000001.11    90067546        .       A       .       32.9944 .       DP=1;MQ0F=0;AF1=0;AC1=0;DP4=0,1,0,0;MQ=34;FQ=-29.9918 GT:PL:DP:AD     0/0:0:1:1

When there is an alternate allele, these are the examples on the file:

NC_000001.11    90067547        .       G       C       5.46383 .       DP=1;SGB=-0.379885;MQ0F=0;AF1=1;AC1=2;DP4=0,0,0,1;MQ=34;FQ=-29.9918   GT:PL:DP:AD     1/1:34,3,0:1:0,1
NC_000001.11    90102132        .       A       G       221.999 .       DP=22;VDB=0.000286129;SGB=-0.69168;MQSBZ=-0.134761;MQ0F=0;AF1=1;AC1=2;DP4=0,0,8,11;MQ=44;FQ=-83.9864  GT:PL:DP:AD     1/1:255,57,0:19:0,19
NC_000001.11    90102276        .       A       C       4.13164 .       DP=1;SGB=-0.379885;MQ0F=0;AF1=1;AC1=2;DP4=0,0,0,1;MQ=41;FQ=-29.9928   GT:PL:DP:AD     0/1:32,3,0:1:0,1
NC_000001.11    90102277        .       G       C       32.7667 .       DP=2;VDB=0.44;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;DP4=0,0,0,2;MQ=40;FQ=-32.988   GT:PL:DP:AD     1/1:64,6,0:2:0,2

Is it okay for it to have such a low read depth and allele depth? I am not sure if something is wrong with my data. Thanks in advance.

pd3 commented 2 months ago

I am afraid this cannot be answered here. Take a look at your bams in IGV and see for yourself what is the coverage of the data. Another useful tool is samtools view.