Pileup

Analysis

• BAM fields description
• Pileup formats comparison
• Pileup potential applications
• Pileup in literature

State-of-the-art implementations

Samtools

• samtools mpileup documentation
• mpileup issue
• mpileup in variant calling pipeline
• samtools, pileup paper
• samtools, bcftools primer

samtools mpileup --region 1:215906528-215906567 \
--fasta-ref human_g1k_v37.fasta NA12891_CEU_sample.bam

GATK

• GATK pileup documentation

docker run --rm -it --entrypoint="java" -v $PWD:/data broadinstitute/picard -jar /usr/picard/picard.jar \
CreateSequenceDictionary \
R=/data/human_g1k_v37.fasta \
O=/data/human_g1k_v37.dict

docker run --rm -it -v /Users/aga/workplace/bds-files/chapter-11-alignment:/data broadinstitute/gatk \
gatk Pileup \
-R /data/human_g1k_v37.fasta \
-I /data/NA12891_CEU_sample.bam \
-O /data/pileup_gatk.pileup

Sambamba

Sambamba korzysta z implementacji samtools - dzieli BAM na kawałki i przekazuje je do samtools mpileup.

• Sambamba documentation

Some benchmarks/baselines

time samtools mpileup -B NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam -o pileup.txt
real    1m2.585s
user    0m59.652s
sys     0m1.312s

wc -l pileup.txt 
58362811 pileup.txt