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.

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)
• The following metada descriptors per sample:
  • readgroup
  • sample_name
  • library_name
  • platform_unit
  • run_date
  • platform_name
  • sequecing_center

Outputs

• Unmapped BAM

bam-to-unmapped-bams :

This WDL converts BAM to unmapped BAMs

Requirements/expectations

• BAM file

Outputs

• Sorted Unmapped BAMs
• Text file listing the unmapped file paths (FOFN)

interleaved-fastq-to-paired-fastq :

This WDL takes in a single interleaved(R1+R2) FASTQ file and separates it into separate R1 and R2 FASTQ (i.e. paired FASTQ) files. Paired FASTQ files are the input format for the tool that generates unmapped BAMs (the format used in most GATK processing and analysis tools).

Requirements/expectations

• Interleaved Fastq file

Outputs

• Separate R1 and R2 FASTQ files (i.e. paired FASTQ)

interleaved-fastq-to-paired-fastq :

This WDL takes in a single interleaved(R1+R2) FASTQ file and separates it into separate R1 and R2 FASTQ (i.e. paired FASTQ) files. Paired FASTQ files are the input format for the tool that generates unmapped BAMs (the format used in most GATK processing and analysis tools).

Requirements/expectations

• Interleaved Fastq file

Outputs

• Separate R1 and R2 FASTQ files (i.e. paired FASTQ)

Software version requirements :

• GATK4 or later
• Samtools 1.3.1
• Picard 2.8.3
• Cromwell version support
  • Successfully tested on v50

Important Notes :

• Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
• The provided JSON is a ready to use example JSON template of the workflow. Users are responsible for reviewing the GATK Tool and Tutorial Documentations to properly set the reference and resource variables.
• For help running workflows on the Google Cloud Platform or locally please view the following tutorial (How to) Execute Workflows from the gatk-workflows Git Organization.
• Relevant reference and resources bundles can be accessed in Resource Bundle.

Contact Us :

• The following material is provided by the Data Science Platforum group at the Broad Institute. Please direct any questions or concerns to one of our forum sites : GATK or Terra.

LICENSING :

Copyright Broad Institute, 2019 | BSD-3 This script is released under the WDL open source code license (BSD-3) (full license text at https://github.com/openwdl/wdl/blob/master/LICENSE). Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script.