run get-reads-alt-unmap.sh in container about hla HOT 3 CLOSED

Second data set had chromosome names as number only, so modified get-reads-alt-unmap.sh to 6 instead of chr6.

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Hi,

xHLA only works with hg38 reference.

The get-reads-alt-unmap.sh script needs to be used when you have a BAM aligned on hg38 reference with alt contigs.

Best,
Astrid

from hla.

Conversion from 37 to 38 worked for me for one bam. I used:
docker run -v ~/bams:/opt/bin/myData -it --entrypoint=/bin/bash humanlongevity/hla
to open a container with my local directory /bams bound to /opt/bin/myData.

I did have to remove the memory detection part of the script as it gave an error at line 17.
And add the fna as @cjieming noted.

On a second data set, though, I'm loosing about half of the reads somewhere in the script. My first go I added a few reads as expected. The only thing I can think of is: when I ran the first time I was using a 37 bam PrintRead to chr6. The first step in the script is to trim, though, so I'm not sure what the issue is.

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