Segmentation fault error while running extractPIRs from ShapeIT

Question

[kirannbishwa01]

I am getting 'segmentation fault error' while trying to run subcommand from ShapeIt

$extractPIRs --bam bamlist --vcf sequence.multiple.vcf.gz --out myPIRsList Reading genotypes in [sequence.multiple.vcf.gz] in VCF format Segmentation fault (core dumped)

This is just a test run using the example file that came with the program. Can't seem to find the cause of it.

Thanks much,

[amitgourav.ghosh12]

Hello! Did you find the reason behind the segmentation fault error? Mine comes without the core dumped statement. It looks like this: /var/spool/pbs/mom_priv/jobs/8948248.wlm01.SC: line 35: 3365 Segmentation fault

Sincerely, Amit

[kirannbishwa01]

That was 3 years ago. Sorry to say, that I dont remember the context of the problem right now.

Not sure, but If you are trying to extract readbackedphased haplotype and runs phasing VCF-SIMPLIFY https://github.com/everestial/VCF-Simplify and other tools in my repo could be helpful.

Thanks,

[amitgourav.ghosh12]

No worries!

Thank you very much for your help.

Sincerely, Amit