extractPIRs is throwing an ERROR
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3.6 years ago
nkausthu ▴ 30

I am getting an error while using extractPIRs as follows

./extractPIRs --bam bamlist --vcf VCF.gz --out

Reading genotypes in [/MOD_recalibrated_variants.vcf.gz] in VCF format
* 477 samples
ERROR: Duplicate site pos=52264013 ref=C alt=T


How can I avoid this kind of scenario? Thank you

extractPIRs SHAPEIT PHASING • 804 views
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Looks like the program is telling you what the error is.

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Yes .. Programs tells that its duplicate site position but its in different chromosome. But I think it wont be correct if I delete one.

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This is rather for further references as this one is really old. If you check their documentation on manual the state:

NOTE : the VCF file should contain SNPs from only one chromosome.

So, it cant handle different chromosomes the same time and you need to split them prior continuing.