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IARCbioinfo / needlestack

Multi-sample somatic variant caller
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Feature: Consider realignment using freebayes/glia/??? #158

Closed mmterpstra closed 4 years ago

mmterpstra commented 7 years ago

Freebayes and the GATK Haplotypecaller perform internal (indel- / left-) realignment over the called samples to improve the calling accuracy / consistency. Consider including this in the workflow or add suggestions to perform this.

mfoll commented 7 years ago

Thanks for the suggestion. We are using ABRA for this purpose (and we have a nextflow pipeline for this too). For modularity reasons we prefer to keep this step out of the needlestack pipeline itself, but you are right, this is something we should add in the documentation (on top of many other things actually)... Do you think this would solve your issue?

mmterpstra commented 7 years ago

Yes add it in the in the manual

  • A set of BAM files (called *.bam) grouped in a single folder along with their index files (called *.bam.bai). A minimum of 20 BAM files is recommended.

to

  • A set of BAM files (called `.bam`) grouped in a single folder along with their index files (called `.bam.bai`). A minimum of 20 BAM files is recommended. Advised it to perform realingment with GATK IndelRealigner or ABRA2