extractPIRs is throwing an ERROR

Question

[nkausthu]

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

[GenoMax]

Looks like the program is telling you what the error is.

[nkausthu]

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

[schmidemanuel]

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.