Very different result between samtools and samblaster

[biozzq]

Dear @GregoryFaust

I am using Lumpy to detect CNV. During preparing the discordant paired-end alignments, I found that the results from the following two pipelines are very different. In my test, the samblaster just reported 0 discordant read pair, but samtools reported many.

(1) samtools view -b -F 1294 sample.bam #refer to the github of lumpy (https://github.com/arq5x/lumpy-sv)
(2) samtools sort -@ 4 -O SAM -n sample.bam | samblaster (Version.0.1.25) -a -e -d $prefix.disc.sam -s $prefix.split.sam -o /dev/null

Hope you can help me, thank you.

Sincerely,
Zheng Zhuqing

[GregoryFaust]

Thanks for bringing this to my attention. Somehow, samblaster V25 does NOT output discordants when used with the acceptDupMarks(-a) option. I have a fix already prepared which I am now testing and will release very soon (this week at latest). In the mean time, samblaster V24 will work for the pipeline you have shown.

As an aside, if your BAM file was aligned with BWA MEM, both of your pipeline fragments shown assume that the -M option was not used. If it was, you will need to use the -M option with samblaster or make a change to the samtools filter specification.

Thanks again.
Greg

[biozzq]

Dear @GregoryFaust

Thank you for reminding. Also I look forward to your update.

Sincerely,
Zhuqing

[GregoryFaust]

Closed in v.0.1.26