Question about command :hlapers bam2fq -b HG00096.bam -m ./hladb/mhc_coords.txt -o HG00096

[alex84425]

In example command:

hlapers bam2fq -b HG00096.bam -m ./hladb/mhc_coords.txt -o HG00096

There is no output callled "HG00096_mhc_1.fq and HG00096_mhc_2.fq" but "HG00096_mhc_unmap_1.fq and HG00096_mhc_unmap_2.fq"

So, It let me confused to do next command.

hlapers genotype -i index/STARMHC -t ./hladb/transcripts_MHC_HLAsupp.fa -1 HG00096_mhc_1.fq -2 HG00096_mhc_2.fq -p 8 -o results/HG00096

Any idea?

[EBYEMJC1]

Hi, I have the same exact question as the output of the previous command was HG00096_mhc_unmap_1.fq and HG00096_mhc_unmap_2.fq. Also, STARMHC is neither a file not a directory within the index. and the .bam file is not provided. I downloaded the bam file from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam but am not sure if it is the right file(and may I ask why that file was chosen?). I am new to installing and using tools so none of this truly makes sense to me, but I have been stuck on this command for the longest time. I tried changing it to:

hlapers genotype -i index -t ./hladb/transcripts_MHC_HLAsupp.fa -1 HG00096_mhc_unmap_1.fq -2 HG00096_mhc_unmap_2.fq -p 8 -o results/HG00096

I am not sure how those changes affect the command or if they even effect the command but when trying it, I just get a continuous buffer