bcftools mpileup v1.15 (wrongly) does not call SNPs when bcftools mpileup v1.10.2 does
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start by reproducing the reported comparison between bcftools mpileup v1.10.2 and v1.15 with the same reference, BAM, and -q 10 -d 15000 options. Inspect the mpileup behavior that changes SNP calling and DP4 values; done requires identifying the cause and confirming the expected call with a regression case.
Written by the indexing model from the issue text.
Description
Hi,
I am using bcftools consensus using v1.15 and got SNPs which were weirdly not called, so I went back to the vcf files.
I have SNPs which I know exist (I am working on simulated reads) which are called when using mpileup from version 1.10.2 and not when using version 1.15, even if a lot of alternative sequences are found (see below). DP4 changes too.
I use the same reference file and the same bam file. I used the options -q 10 -d 15000 in both cases.
For instance:
with v1.10.2
gene1 51 . A T 22.268 . DP=17932;VDB=0;SGB=-0.693147;RPB=1.51927e-05;MQB=0;BQB=0.0361916;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4774,0,3504,0;MQ=49 GT:PL 0/1:55,0,70
with v1.15
gene1 51 . A . 17.2269 . DP=17932;VDB=0;SGB=-0.693147;RPBZ=-6.58337;MQBZ=-88.0103;BQBZ=-2.09656;SCBZ=5.45755;FS=0;MQ0F=0;AN=2;DP4=10424,0,7508,0;MQ=49 GT 0/0
I read manual pages for both versions and cannot find a default parameter which changed.
Thanks a lot!
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