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eblerjana / whatshap-polyphase-experiments

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whatshap_haplotag #1

Open lxz1019 opened 2 years ago

lxz1019 commented 2 years ago

hi, I found that there is a "whatshap_haplotag" in the line "{whatshap_haplotag} split {input.bam} {input.tsv} --output-h1 {output.bamh1} --output-h2 {output.bamh2} --output-h3 {output.bamh3} --output-h4 {output.bamh4} &> {log}" of potato Snakefile, could you please tell me what does this "whatshap_haplotag" mean? Is it another version of whatshap haplotag? I'd like to refer to your pipeline for my polyploid data, many thanks.

schrins commented 2 years ago

I suspect this is a typo and it should just be {whatshap}. What follows after is a regular whatshap command in both cases.

lxz1019 commented 2 years ago

》》》shell("{whatshap_haplotag} haplotag {output.vcf} {input.bam} --reference {input.reference} --ploidy {params.ploidy} --output-haplotag-list {output.tsv} -o {output.bam} &> {log}") 》》》"{whatshap_haplotag} split {input.bam} {input.tsv} --output-h1 {output.bamh1} --output-h2 {output.bamh2} --output-h3 {output.bamh3} --output-h4 {output.bamh4} &> {log}"

it seems that the current haplotag didn't support this "--ploidy", as well as to the "--output-h3 & --output-h4" for the whatshap split, so which version of whatshap haplotag and whatshap split are used to deal with potato? Can you share it with me, many thanks.