Pindel results not normalized

[elleira]

Hi!
The way Hydra is set up right now pindel is locateded in the cnv_sv module, this results in that the pindel vcf is missed by VT and is not left aligned, normalized or decompose. The pindel vcf also does not have an AF or DP field in the INFO column. At least in Uppsala we are treating the pindel results more like a "normal" SNV caller and would prefer that the vcf is as similar as the vcfs coming out from snv_indels module (left aligned, decomposed, af-, dp-field etc).

Is normalization something everyone want or should i fix it locally for Uppsala?

[maehler]

I can't really say I have a strong opinion on this since I don't have enough experience with these things, but instinctively I don't think that normalizing the output would be a bad thing.

A possible implementation could be to create modified versions of the relevant rules in the main snakefile, something like this:

use rule vt_decompose as pindel_vt_decompose with:
    input:
        "cnv_sv/pindel_vcf/{sample}_{type}.no_tc.vcf",
    output:
        temp("cnv_sv/pindel_vcf/{sample}_{type}.no_tc.normalized.vcf"),
    log:
        "cnv_sv/pindel_vcf/{sample}_{type}.no_tc.normalized.vcf.log",
    benchmark:
        repeat(
            "cnv_sv/pindel_vcf/{sample}_{type}.no_tc.normalized.vcf.benchmark.log",
            config.get("pindel_vt_decompose", {}).get("benchmark_repeats", 1),
        )

Then we can also have a separate entry for the pindel-specific normalization if we think that this would be useful.