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Add NGSCheckMate #993
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Add NGSCheckMate #993
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Inclusion probably a call for @drpatelh, but a couple of minor comments in the meantime
@@ -768,6 +772,15 @@ workflow RNASEQ { | |||
ch_versions = ch_versions.mix(DUPRADAR.out.versions.first()) | |||
} | |||
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if (params.ngscheckmate_bed) { | |||
BAM_NGSCHECKMATE ( |
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Is there any way the output could be baked into the MultiQC report?
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That has been suggested over in sarek too, something I could consider.
docs/output.md
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</details> | ||
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[NGSCheckMate](https://github.com/parklab/NGSCheckMate) is a tool to verify that samples come from the same individual, by examining a set of single nucleotide polymorphisms (SNPs). This calculates correlations between the samples, and then applies a depth-dependent model of allele fractions to call samples as being related or not. The principal output is a dendrogram, where samples that are . |
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Unfinished sentence
ch_versions = ch_versions.mix(BCFTOOLS_MPILEUP.out.versions) | ||
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BCFTOOLS_MPILEUP | ||
.out |
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Indent the ops (here and below)?
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This is in the nf-core subworkflow, but I'll try and remember to do it when I convert to nf-test.
Hmm, we could check for the existence of chr mismatching, that would be relatively simple I guess? |
This PR adds the NGSCheckMate tool to the pipeline. I find this an essential tool and part of my initial QC for all sequencing we perform. This tool takes a bed file with a set of SNPs and tries to determine if samples come from the same individuals. Developed and generally used in humans (there are SNP bed files for hg19/hg38/GRCh37/GRCh38 available), but could be used in other species if a suitable set of common SNPs was provided.
This should be configured to run automatically on GRCh37/38, hg37/hg38 I think needs the files adding to igenomes - need to check.
This ensures that no sample swaps have occurred by checking:
It works on human derived cell lines, but won't separate different treatments applied to the same cell line.
Testing.
I have used a bed file on the test datasets to get it to run on yeast, haven't tried the full tests yet.
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).