bcftools mpileup resulting in downstream unparsable vcf record with allele M
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start with the reported bcftools mpileup command, the combined BAM inputs, and the generated record at AM270990.1:518406 containing allele M. Compare the combined output with the single VCF files and determine whether bcftools produces an invalid record or whether the downstream GATK error reflects an input or compatibility issue; a complete reproduction and a confirmed valid output would define done.
Written by the indexing model from the issue text.
Description
Hello,
I am currently trying to call SNPs to generate an alternative fasta sequence. Whenever I combine BAM files using bcftools mpileup (bcftools version 1.20) everything runs properly until I try to use GATK IndexFeautureFile code and them I am left with an error of "The provided VCF file is malformed at approximately line number 25863560: unparsable vcf record with allele M".
When I check the combined VCF file I do see the M allele (see below)
AM270990.1 518406 . M MA 999 PASS INDEL;IDV=1;IMF=0.0714286;DP=77;VDB=3.06326e-29;SGB=-3.22514;RPBZ=-2.95767;MQBZ=0.986013;MQSBZ=0.930949;SCBZ=0;MQ0F=0; AF1=1;AC1=5;DP4=1,1,65,8;MQ=42;FQ=-243.559;PV4=0.227027,1,1,1 GT:PL 1:255,42,0 1:243,48,0 1:255,29,0 1:246,60,0 1:200,24,0
When I check the single VCF files (non combined) I do not see this M allele or position 518406 on chr AM270990.1
Code: bcftools mpileup -Ou -f Aniger_Reference_Files/GCA_000002855.2_ASM285v2_genomic.fna Sorted_Mapped_Trimmed_CTWT-1A.bam Sorted_Mapped_Trimmed_CTWT-1B.bam > Sorted_Mapped_Trimmed_CTWT_AB.bcf
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