Question: Unmapping Alternative reads
0
gravatar for godth13teen
7 months ago by
godth13teen50
godth13teen50 wrote:

Hi, I want to do some HLA typing, most of the tools require the bam file is aligned to primary genome without alternative read handling. From the International Genome Sample Resource project, I can get the high coverage file, but they are all aligned to primary genome with hla, decoy and alternative reads.

I want to unmap those alternative reads, I tried this script https://github.com/humanlongevity/HLA/blob/master/bin/get-reads-alt-unmap.sh, but there are some technical problems, so I want to know is there any other way or tools to do this task?

Thank you very much.

dna alignment • 202 views
ADD COMMENTlink written 7 months ago by godth13teen50

there are some technical problems

What kind of problems. It may be easy to solve them.

ADD REPLYlink written 7 months ago by genomax92k

Hi,

I made a github issue in here: https://github.com/humanlongevity/HLA/issues/51

In short, there's an [E::bwa_idx_load_from_disk] fail to locate the index files error, and the script output nothing

ADD REPLYlink written 7 months ago by godth13teen50

Have you created an index for the BAM files you downloaded (samtools index, you would likely need to samtools sort before that)? If you use latest samtools then sort --write-index to do this in one step.

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax92k

yes, I made the index *.bam.bai for the bam file beforehand

ADD REPLYlink written 7 months ago by godth13teen50

Looks like you did not name sort (samtools sort -n) your files before indexing them.

ADD REPLYlink modified 7 months ago • written 7 months ago by genomax92k

The bam file is already sorted:

samtools view -H HG02082.final.bam |grep "@HD"
@HD     VN:1.5  GO:none SO:coordinate
ADD REPLYlink written 7 months ago by godth13teen50

but you mean that I need to sort it by name, not coordinate, am I right?

ADD REPLYlink written 7 months ago by godth13teen50

Based on the errors you posted in GitHub issue, yes.

ADD REPLYlink written 7 months ago by genomax92k

I tried sorting it by queryname and index it, but the script still does not work

ADD REPLYlink written 7 months ago by godth13teen50
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