Segmentation fault error while running extractPIRs from ShapeIT
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4.9 years ago
kirannbishwa01 ★ 1.3k

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,

ShapeIT segmentation fault error vcf bam • 1.8k views
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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

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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,

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No worries!

Thank you very much for your help.

Sincerely, Amit

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