GATK CallableLoci

GATK (v3.8-1) CallableLoci is used to identify callable regions to create high confidence region for Quartet reference small variants datasets.

Command line used in this app:

java -jar /usr/GenomeAnalysisTK.jar \
		-T CallableLoci \
		-R ${ref_dir}/${fasta} \
		-I ${bam} \
		--maxDepth 300 \
		--maxFractionOfReadsWithLowMAPQ 0.1 \
		--maxLowMAPQ 1 \
		--minBaseQuality 20 \
		--minMappingQuality 20 \
		--minDepth 5 \
		--minDepthForLowMAPQ 10 \
		-summary ${sample}_table.txt \
		-o ${sample}_callable_status.bed

Parameters explanation:

--maxDepth 300, If the QC+ depth exceed this value, the site is considered to have EXCESSIVE_DEPTH.

--maxFractionOfReadsWithLowMAPQ 0.1, If the number of reads at this site is greater than minDepthForLowMAPQ and the fraction of reads with low mapping quality exceeds this fraction then the site has POOR_MAPPING_QUALITY.

--maxLowMAPQ 1, Maximum value for (mapping quality) MAPQ to be considered a problematic mapped read. The gap between this value and mmq are reads that are not sufficiently well mapped for calling but aren’t indicative of mapping problems. For example, if maxLowMAPQ = 1 and mmq = 20, then reads with MAPQ == 0 are poorly mapped, MAPQ >= 20 are considered as contributing to calling, where reads with MAPQ >= 1 and < 20 are not bad in and of themselves but aren’t sufficiently good to contribute to calling. In effect this reads are invisible, driving the base to the NO_ or LOW_COVERAGE states.

--minBaseQuality 20, Minimum quality of bases to count towards depth. Bases with less than minBaseQuality are viewed as not sufficiently high quality to contribute to the PASS state.

--minMappingQuality 20, Minimum mapping quality of reads to count towards depth. Reads with MAPQ > minMappingQuality are treated as usable for variation detection, contributing to the PASS state.

--minDepth 5, Minimum QC+ read depth before a locus is considered callable If the number of QC+ bases (on reads with MAPQ > minMappingQuality and with base quality > minBaseQuality) exceeds this value and is less than maxDepth the site is considered PASS.

--minDepthForLowMAPQ 10, Minimum read depth before a locus is considered a potential candidate for poorly mapped We don’t want to consider a site as POOR_MAPPING_QUALITY just because it has two reads, and one is MAPQ. We won’t assign a site to the POOR_MAPPING_QUALITY state unless there are at least minDepthForLowMAPQ reads covering the site.

Per sample running time

Settings:

Disk size: 400

Cluster: OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc

sample: 30x WGS

2h30min