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mourisl / T1K

T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with bulk or single-cell RNA-seq, WGS or WES data.
MIT License
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How to output a bam file #14

Closed Ritabear closed 1 year ago

Ritabear commented 1 year ago

Hi~ I need to watch the bam file by IGV. Therefore, I hope the t1k can output a bam file.

Thanks a lot for the help!

mourisl commented 1 year ago

BAM file is not easy to generate. I think the best way is to filter your reference file, e.g. hlaref{dna,rna}.fa using the representative alleles from the t1k_allele.tsv file, and then extract the allele sequences from the reference fasta file, then build a BWA/Bowtie index and run the alignment on the subset of alleles.

Ritabear commented 1 year ago

Thank you so much for helping out. Sorry, English is not my mother tongue. It seems a bit rude to speak like this above. I am deeply sorry, but I don't mean to offend.

mourisl commented 1 year ago

Oh, I was not offended at all. It's just that the BAM file is not straightforward to generate, and using BWA/Bowtie is a more straightforward solution.