seq-format-conversion

Workflows for converting between sequence data formats

cram-to-bam :

This script should convert a CRAM to SAM to BAM and output a BAM, BAM Index, and validation report to a Google bucket. If you'd like to do this on multiple CRAMS, create a sample set in the Data tab.
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.

Requirements/expectations

• Cram file

Outputs

• Bam file and index
• Validation report

paired-fastq-to-unmapped-bam :

This WDL converts paired FASTQ to uBAM and adds read group information

Requirements/expectations

• Pair-end sequencing data in FASTQ format (one file per orientation)
• One or more read groups, one per pair of FASTQ files

Outputs

• Set of unmapped BAMs, one per read group

Software version requirements :

Cromwell version support

• Successfully tested on v30.2
• Does not work on versions < v23 due to output syntax