CollectWgsMetrics, samtools stats and bamqc do not use BAM index files

[sorelfitzgibbon]

Since the documentation was not entirely clear, I confirmed there was no significant speed up if BAM file indices are provided:

#!/bin/bash
module load samtools

time docker run \
    -u $(id -u):$(id -g)  \
    -v /hot:/hot \
    ghcr.io/uclahs-cds/picard:3.1.0 \
    java -Xms4G -jar /usr/local/share/picard-slim-3.1.0-0/picard.jar CollectWgsMetrics \
    INPUT=/hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-SQC-DNA/tmp.bam \
    OUTPUT=/hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-SQC-DNA/cwm-no-bai-1.txt \
    REFERENCE_SEQUENCE=/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta


time docker run \
    -u $(id -u):$(id -g)  \
    -v /hot:/hot \
    ghcr.io/uclahs-cds/picard:3.1.0 \
    java -Xms4G -jar /usr/local/share/picard-slim-3.1.0-0/picard.jar CollectWgsMetrics \
    INPUT=/hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-SQC-DNA/tmp.bam \
    OUTPUT=/hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-SQC-DNA/cwm-no-bai-2.txt \
    REFERENCE_SEQUENCE=/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta

time samtools stats /hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-SQC-DNA/tmp.bam > stats-no-bai-1.txt
time samtools stats --remove-dups /hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-SQC-DNA/tmp.bam > stats-rmdups-no-bai-1.txt

time samtools index /hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-SQC-DNA/tmp.bam

time docker run \
    -u $(id -u):$(id -g)  \
    -v /hot:/hot \
    ghcr.io/uclahs-cds/picard:3.1.0 \
    java -Xms4G -jar /usr/local/share/picard-slim-3.1.0-0/picard.jar CollectWgsMetrics \
    INPUT=/hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-SQC-DNA/tmp.bam \
    OUTPUT=/hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-SQC-DNA/cwm-with-bai-1.txt \
    REFERENCE_SEQUENCE=/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta

time samtools stats /hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-SQC-DNA/tmp.bam > stats-with-bai-1.txt
time samtools stats --remove-dups /hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-SQC-DNA/tmp.bam > stats-rmdups-with-bai-1.txt

Time results:
real 20m23.953s
real 19m52.260s
real 16m55.590s
real 5m53.250s
real 3m39.688s
real 19m1.358s
real 5m52.700s
real 6m32.637s