Samtools-hybrid

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What is samtools-hybrid?

samtools-hybrid is a modified version of samtools.

This hybrid version of samtools is essentially samtools version 0.1.7a (r510), except the 0.1.7a bgzf logic and "calmd" functionality have been replaced with the bgzf and "calmd" from samtools revision r983.

The original samtools-hybrid merged in version 0.1.12a (r862), but it has since been upgraded to r983 to bring in the enhanced BAQ logic.

This hybrid version does not provide the samtools "mpileup" SNP calling capability, nor the "idxstats" and "reheader" capabilities that are present in the full version 0.1.12a and later.

Why was samtools-hybrid created?

The purpose is to provide in one executable Heng Li's BAQ base call quality score adjustment functionality from "calmd", as well as to output valid .glf format when using 'samtools pileup -g'.

Some of our tools require both of these methods and since there is not a version of samtools that supports both pileup generating GLF files and the BAQ logic, we created this hybrid version so we could release single version of samtools for use by our tools.

Where can I get samtools-hybrid?

That code can be downloaded at: https://github.com/statgen/samtools-0.1.7a-hybrid

Alternatively, you can download the file here: samtools-0.1.7a-hybrid.v1.1.1.tgz - Released 7/25/2013

Troubleshooting

If you have additional questions or comments, please email Mary Kate Wing (mktrost@umich.edu).

I get a 'floating point exception' with a command like samtools-hybrid pileup $bam -g -f $fasta > $bam.glf
One potential issue is that the fasta index file (.fai file) is either not correct for the fasta file or it is not in the exact format that samtools-hybrid expects. Try removing the .fai file and let samtools-hybrid regenerate the file. That will ensure that samtools-hybrid is reading the file in the format it expects.