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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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hg38 patch - "MD tag not present" #67

Open bailey-c opened 4 years ago

bailey-c commented 4 years ago

Dear Viraj,

We are running Amplicon Architect on WGS tumour samples aligned to the GRCh38 build. Unfortunately I am getting the error "MD tag not present", which was not an issue when run with the hg37 patch.

I'm guessing this has something to do with the aligner that we are using (we are using Isaac aligner and not BWA). Is there a way of using the GRCh38 patch in a way that excludes the entropy calculation and does not require the MD tag?

Best

Chris

oneillkza commented 4 years ago

I'm not the maintainer or anything, but I've had issues with missing MD tags and other tools in the past. One solution is to use samtools to add the MD tag after alignment: http://www.htslib.org/doc/samtools-calmd.html

jluebeck commented 4 years ago

If you do not want to add the MD tag, I have been maintaining a version of AA which has been tested on BAMs generated by Illumina's Isaac aligner without MD tags, available here. This is the same fork which now supports hg38-aligned data.