Question: What Are The Differences Between Gatk'S Reducebam And Cram?
1
gravatar for 14134125465346445
6.4 years ago by
United Kingdom
141341254653464453.5k wrote:

What are the differences between GATK's reducebam and CRAM?

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_compression_reducereads_ReduceReads.html

Are these essentially two different implementations towards the same goal?

gatk next-gen bam • 2.3k views
ADD COMMENTlink modified 6.4 years ago by vadim.zalunin40 • written 6.4 years ago by 141341254653464453.5k
3
gravatar for vadim.zalunin
6.4 years ago by
vadim.zalunin40 wrote:

Reads in a reduced BAM are made up of differences between the original reads and the reference sequence used for alignment whereas CRAM format preserves placement and bases of original reads. Basically lossless CRAM can be restored to original BAM. Reduced BAM approach allows to analyze more sample at once than regular BAM but the data cannot be re-aligned afaik, therefore it is reference biased.

To use CRAM files you would need a special software: java implementation https://github.com/enasequence/cramtools or C implementation done by James Bonfield from Sanger Institute http://staden.svn.sourceforge.net/

There is a notion to make CRAM files compatible with existing tools using common CRAM-BAM API. For example picard tools should work on CRAM and BAM files given the cramtools jar is used.

ADD COMMENTlink written 6.4 years ago by vadim.zalunin40
2
gravatar for Pierre Lindenbaum
6.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

The GATK produces a file that is still a BAM.

CRAM is another format, your tools (samtools) migth not be able to handle it.

ADD COMMENTlink written 6.4 years ago by Pierre Lindenbaum123k
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