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Can GATK accepts more than one bed file while computing depth of coverage?

NandaNanda CanadaMember

Group1.BAMfiles.list has three BAM files:
Sample_001/SAM001.clean.dedup.recal.bam
Sample_002/SAM002.clean.dedup.recal.bam
Sample_003/SAM003.clean.dedup.recal.bam

Group1.BED has three BED files:
S1_10.intervals.b37.bed
S2_10.intervals.b37.bed
S3_10.intervals.b37.bed

java -Xmx12g -jar /gatk/GenomeAnalysisTK-3.8.0/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar \
-T DepthOfCoverage \
-R reference_genome.fa \
-I Group1.BAMfiles.list \
-L Group1.BED \
-dt BY_SAMPLE -dcov 5000 -l INFO \
--omitDepthOutputAtEachBase --omitLocusTable \
--minBaseQuality 0 --minMappingQuality 20 \
--start 1 --stop 5000 --nBins 200 \
--includeRefNSites --countType COUNT_FRAGMENTS \
-o Group1.DATA.txt

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator admin

    Hi @Nanda,

    Yes, you need only additionally specify each intervals file with -L.

  • NandaNanda CanadaMember

    Does GATK automatically map the interval lists to the corresponding BAM files?
    For example,
    Case1: Each BAM file has three different interval list
    Group1.BED has three BED files:
    S1_10.intervals.b37.bed
    S2_10.intervals.b37.bed
    S3_10.intervals.b37.bed

    -L Group1.BED
    -L Group2.BED
    -L Group3.BED

    Case2: S1_10 and S2_10 has sample BED file but S3_10 has different BED file.
    Group1.BED has three BED files:
    S1_10.intervals.b37.bed
    S2_10.intervals.b37.bed
    S3_10.intervals.b37.bed

    -L Group1.BED
    -L Group2.BED
    -L Group2.BED

  • shleeshlee CambridgeMember, Broadie, Moderator admin

    @Nanda, not that I know of but you can certainly give it a try to confirm. GATK3's -L option is described here.

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