github.com/shengqh/seq-format-conversion/Multi-Paired-FASTQ-to-Multi-Unmapped-BAM

seq-format-conversion

Workflows for converting between sequence data formats

cram-to-bam :

This script should convert a CRAM to SAM to BAM and outputs a BAM, BAM Index,
and validation report.
The reason this approach was chosen instead of converting CRAM to BAM directly
using Samtools is because Samtools 1.3 produces incorrect bins due to an old version of htslib
included in the package. Samtools versions 1.4 & 1.5 have an NM issue that
causes them to not validate with Picard.


This is a companion discussion topic for the original entry at github.com/shengqh/seq-format-conversion/Multi-Paired-FASTQ-to-Multi-Unmapped-BAM