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sanger-tol / variantcalling

Nextflow DSL2 pipeline to call variants on long read alignment.
https://pipelines.tol.sanger.ac.uk/variantcalling
MIT License
3 stars 2 forks source link

Variant calling with short read data #46

Open priyanka-surana opened 1 year ago

priyanka-surana commented 1 year ago

Description of feature

Variant calling for short read data. Tools considered: FreeBayes, GATK, samtools mpileup

muffato commented 11 months ago

After talking to the Cardiff team, who analysed otter resequencing data, we should go with GATK, which has a standard and complete pipeline (incl. joint-calling) – and investigate nf-core/sarek, which should be doing a lot of that.

muffato commented 11 months ago

After talking to the HumGen informatics team, it seems sarek can't do per-individual variant calling and joint-calling in the same run. It has to be run twice. They're working on a fork that could do that in the same pipeline run.

muffato commented 5 months ago

Waiting for the outcome of #79