extractPIRs is throwing an ERROR
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
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GenoMax
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nkausthu •
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nkausthu •
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Looks like the program is telling you what the error is.
Yes .. Programs tells that its duplicate site position but its in different chromosome. But I think it wont be correct if I delete one.
This is rather for further references as this one is really old. If you check their documentation on manual the state:
So, it cant handle different chromosomes the same time and you need to split them prior continuing.