VCFAnnoBam

Motivation

Annotate a VCF with the Coverage statistics of a BAM file + BED file of capture. It uses the Cigar string instead of the start/end to get the voverage

Compilation

See also Compilation

$ make vcfannobam

##Options

Option	Description
BEDILE=File	BED File capture. Required.
BAMFILE=File	indexed BAM File. This option must be specified at least 1 times.
MMQ=Integer	min mapping quality Default value: 0. This option can be set to 'null' to clear the default value.
MIN_COVERAGE=Integer	min coverage to say the position is not covered Default value: 0. This option can be set to 'null' to clear the default value.
IN=String	VCF file/URL to process. Default stdin. Default value: null.
OUT=File	VCF file to generate. Default stdout. Default value: null.

##Example

$  java -jar dist/vcfannobam.jar \
		BAM=input.bam\
		IN=input.vcf.gz \
		BED=capture.bed \
		VALIDATION_STRINGENCY=SILENT

(...)
##INFO=<ID=CAPTURE,Number=1,Type=String,Description="Capture stats: Format is (start|end|mean|min|max|length|not_covered|percent_covered) ">
(...)
2	16100665	.	A	T	13261.77	.	CAPTURE=16100619|16100715|1331.96|1026.0|1773.0|97|0|100
2	178395141	.	T	A	1940.77	.	CAPTURE=178394991|178395199|193.11|100.0|276.0|209|0|100
(...)