Hello,
I ran mpileup on a bam aligned to GrCH38, and my mpileup looks like all of the
alignments are forward strand (all ‘.' and upper case, no ‘,’ or lower case).
Here is how I generated my bam and mpileup:
bwa.kit/run-bwamem -s -d -R "@RG\tID:${ID1}\tLB=L001\tSM:${SAMPLE_NAME}" -o
${OUT_PATH}/${SAMPLE_NAME}.1 ${REF} ${FASTQ1R1} ${FASTQ1R2} | sh
bwa.kit/samtools merge -b bamlist.txt
bwa.kit/samtools mpileup -r chr17 --rf 0x2 --ff 0x400 -O -s -f hs38DH.fa
mybam.bam
When I run "samtools flagstat mybam.bam” it looks like there are about equal
reads on the forward and reverse strand, and 98% properly paired. Has anyone
else run into this issue?
Thanks,
Rebecca
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