bcbio.variation.recall.square — bcbio.variation.recall 0.2.0

Performing squaring off of variant call sets, recalling at all sample positions. This converts a merged dataset with no calls at positions not assessed in the sample, into a fully 'square' merged callset with reference calls at positions without evidence for a variant, distinguishing true no-calls from reference calls.

-main clj

(-main & args)

by-region clj

(by-region vcf-files bam-files region ref-file dirs out-file config)

Square off a genomic region, identifying variants from all samples and recalling at uncalled positions.

• Identifies all called variants from all samples
• For each sample, square off using sample-by-region
• Merge all variant files in the region together.

combine-vcfs clj

(combine-vcfs orig-vcf-files bam-files ref-file out-file config)

Combine VCF files with squaring off by recalling at uncalled variant positions.

recall-variants clj multimethod

Recall variants only at positions in provided input VCF file, using multiple callers.

sample-to-bam-map clj

(sample-to-bam-map bam-files ref-file cache-dir)

Prepare a map of sample names to BAM files.

subset-sample-region clj

(subset-sample-region vcf-file sample region out-file)

Subset the input file to the given region and sample.

union-variants clj

(union-variants vcf-files region ref-file out-file)

vcf->bcftools-call-input clj

(vcf->bcftools-call-input vcf-file)

Convert a VCF input file into the custom format needed for bcftools call. XXX Not currently used as constrained calling is broken in samtools 1.0 for multiple positions.