Hello community,
I want to conduct joint sample analysis by HaplotyeCaller using parabrcks.
In the following web page,
“The argument may also be a local folder containing several BAM files.” is discribed in documentation for haplotypecaller option, “–in-bam”.
But, several sample call did not work as follows.
pbrun haplotypecaller
–tmp-dir /work/
–htvc-low-memory
–ref ./genome.fa
–haplotypecaller-options ‘-A StrandBiasBySample’
–in-bam ./test/
–out-variants out.vcf &
Error messeage was as follows.
[E::hts_open_format] Failed to open file “/xxx/test” : Is a directory
In addition, when we ran haplotypecaller with multiple bams specified, a vcf was created for the first bam only.
There’s something I could do?
Thanks in advice.
Best,