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arshajii / ema

Fast & accurate alignment of barcoded short-reads
http://ema.csail.mit.edu
MIT License
32 stars 7 forks source link

10X Long Ranger with EMA BAM #26

Closed jasmine-alvarez closed 5 years ago

jasmine-alvarez commented 5 years ago

Hello,

We have barcoded short-read samples that we aligned with EMA and we are interested in using the resulting BAM file for the 10x Long Ranger pipeline. Specifically, we would like to provide the EMA BAM file as input for Long Ranger's structural variant calling and other downstream analyses. For single variants we already used GATK's HaplotypeCaller (v4.0.8.1) on the BAM file as described in your experimental pipeline. It seems that this pipeline only accepts fastq files for input and we would like to know if it would be possible to instead use results from EMA.

inumanag commented 5 years ago

Hi @wjalvarez :

We have already tried to integrate EMA with Long Ranger before but it turned out to be futile exercise as Long Ranger is (1) not documented and (2) relies way too much on internal flags and files that would take way too much to reverse engineer on our side (it's not as simple as BAM replacement, sadly).

Maybe we should ask Long Ranger developers to support BAM input.