Commit 7afed00b authored by Sander Bollen's avatar Sander Bollen
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gcoverage docs

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......@@ -63,4 +63,42 @@ Options:
-i, --input FILE Input VCF file [required]
--help Show this message and exit.
### vtools-gcoverage
Collect coverage metrics over a gVCF file for every exon or every transcript
in a refFlat file. This assumes the input VCF file is at least similar to
GATK's gVCF files. gVCF files are only expected to have one sample; if
your input file contains multiple samples, we simply take the first only.
Output is a simple TSV file with the following columns
| column | meaning |
| ------ | ------- |
| exon | exon number |
| gene | gene name / symbol / id |
| mean_dp | mean DP value over the exon |
| mean_gq | mean GQ value over the exon* |
| median_dp | median DP value over the exon |
| median_gq | median GQ value over the exon |
| perc_at_least_{10, 20, 30, 50, 100}_dp | Percentage of exon with DP value over value |
| perc_at_least_{10, 29, 30, 50, 90}_gq | Percentage of exon with GQ value over exon |
| transcript | transcript name / symbol / id |
*: mean GQ value is computed by first calculating the P-value of all GQ
values, then calculating the mean over these P-values, and lastly
converting this number back to a phred score.
#### Usage
Usage: vtools-gcoverage [OPTIONS]
-I, --input-gvcf PATH Path to input VCF file [required]
-R, --refflat-file PATH Path to refFlat file [required]
--per-exon / --per-transcript Collect metrics per exon or per transcript
--help Show this message and exit.
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