verifyBamID generating error 'VcfFileException'
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Entering edit mode
7.1 years ago
MAPK ★ 2.0k

Hello. I was trying to run this too called verifybamID to detect sample contamination with the command below, but for some reason it generates the error below termed as 'VcfFileException'. Someone please explain me the issue here?

command:

 ./verifyBamID --vcf /media/SNPs/AOGC-Genotyping.output.recalibrated.filtered.vcf --bam /media/BAM/AOGC-02-0010_C0J43ACXX-4-13.ReCal.sort.bam --out test --verbose --ignoreRG

Error:

Opening VCF file /media/SNPs/AOGC-Genotyping.output.recalibrated.filtered.vcf
Total of 1 out of 1 individuals successfully matched IDs
WARNING : Skipping marker chr1:17172 with multiple alternative alleles
terminate called after throwing an instance of 'VcfFileException'
  what():  # values = ./.:.:45 do not match with # fields in FORMAT field = 5 at sampleIndex = 133 See line 228.
Aborted (core dumped)
verifybamID • 1.4k views
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Entering edit mode
6.8 years ago
Prash ▴ 190

Hi MAPK, I am not sure if you solved this.

But it appears to me that the VCF is not sorted. Is your file with multiple samples?

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