Recommended alignment pipeline for Delly

[Richard de Borja]

Good morning,

I was curious if there was a recommended pipeline for aligning FASTQ files to BAM files and any post processing (i.e. sorting, marking duplicates, quality score recalibration, local realignment) for use with Delly.

Regards,

Richard

[Tobias Rausch]

Hi,

A coordinate sorted bam file is required (samtools sort). Quality score recalibration or local indel realignment is not required but it is also not harmful. If duplicates are marked, Delly ignores them but Delly also filters duplicates internally so it is again not required. 

Delly should be fairly robust regarding the specific aligner that was used as long as they follow the SAM specification. We never benchmarked which aligner works best with Delly so I cannot really give a recommendation here. Internally we mostly used it with bwa aln, bwa mem and eland alignments.

Best, Tobias

 

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[Richard de Borja]

Does using the -M flag (i.e. mark shorter split hits as secondary) in BWA mem cause issue?  I'm in the process of realigning our data which originally included the -M flag (used with Lumpy) and noticed a number of discrepancies with discordant pairs between IGV results and output from Delly.

[Tobias Rausch]

Hi,

For Delly, -M is not required anymore for bwa mem because a while ago the SAM spec was augmented by a supplementary alignment flag. This flag is now used by bwa mem and Delly is also aware of this new flag.

Best, Tobias