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WenjinGudaisy / SearcHPV

An HPV integration point detection tool for targeted capture sequencing data
MIT License
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Wrong input filename in indel.alignment.sh sub command #3

Open jonbra opened 2 years ago

jonbra commented 2 years ago

Samtools index takes as input the file alignment.RG.sort.bam, but the previous sort command generates a file called alignment.RG.sort

WenjinGudaisy commented 2 years ago

Hi,

I've just updated the usage and the package. Can you try again with the new manual? Now we could set up a conda environment and automatically install all the third-party tools.

jonbra commented 2 years ago

Thanks, the conda environment works. Although I had to build samtools 1.5 separately on my Linux machine (it's a common issue when installing samtools through conda).

Nevertheless, my issue was that the samtools sort command produces a file called alignment.RG.sort, while it should be alignment.RG.sort.bam. Otherwise the RealignerTargetCreator fails. In addition, I think that the samtools sort command should include the -o option before the output file name (see my other issue).

WenjinGudaisy commented 2 years ago

Hi,

I just updated and fixed the problem of samtools. Thanks for bringing up the problem! Please use the latest version of "environment.yml" file. Now we are using samtools 1.9, since other versions may have problems when installing using Conda. And I updated all the samtools commands as well.

Thanks, Wenjin