Segmentation fault using verifyBAMID (vb1.1.3)

[haroo...@gmail.com]

I ran the verifyBAMID (vb1.1.3) in order to check for contamination and sample swap in RNASeq samples, using the following command:

$VERIFY_BAM_ID_HOME/bin/verifyBamID --bam $bamfile --vcf $genotype --ignoreRG --out $output --best --verbose

where

bamfile : a single sample RNA-Seq alignment file in BAM format - across all chromosomes

genotype: multi sample genotype file in VCF format (n=6000+ samples) across all chromosomes - around 6 million markers

The tool gives an error 'Segmentation fault'

Reading 2180000 markers from VCF file
Reading 2190000 markers from VCF file
Reading 2200000 markers from VCF file
/path/1545943765.581218.shell: line 1: 16092 Segmentation fault

The tool works fine when I subset the same VCF file (n=3 samples). I was wondering if there was any requirements for VCF file (in terms of number of samples/genotypes and number of markers).

Any advise will be highly appreciated.

2.6.0.0

[Hyun Min Kang]

I guess 6,000 samples are way too many and probably failing on memory allocation. Since it is RNA-seq, I suggest to use VCF files focusing on exons, and it might run fine.

--
You received this message because you are subscribed to the Google Groups "verifyBamID" group.
To unsubscribe from this group and stop receiving emails from it, send an email to verifybamid...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.