5.7.0 - bwa-postalt + tag pass through

• bwa-postalt via option
  • alt aware mapping provided *.alt file provided during mapping
• Retain tags from BAM/CRAM input when mapping
  • Specifically to aid retention of barcode info
  • Equally useful for capturing tags from fastq header lines.

5.6.1 - htslib/samtools 1.12

Docker image (singularity compatible) is available: quay.io/wtsicgp/pcap-core:5.6.1.

• htslib 1.12
• samtools 1.12

5.6.0 - bwa-mem2 v2.2.1

See 5.6.1

Incorporates the highly comparable bwa-mem2 release, v2.2.1.

High confidence in exact replication of legacy BWA for human WGS data following extensive testing. Please see thread on bwa-mem2 tracker.

Minor edits to installation for convenience.

5.4.0 - maintenance

• Update base image of docker to cgpbigwig 1.5.0
• Update to htslib 1.11
• Update to samtools 1.11 - to handle long running markdup issue

5.3.0 - Illumina style paired fastq file names

Paired fastq inputs now accept the Illumina style filename suffixes:

• *_R1_001.fastq.gz + *_R2_001.fastq.gz

Old behaviour is retained.

Thanks go to @ckandoth for the work on this.

5.2.0 - legacy mode

Responding to user request to allow legacy mapping/markdup methods while including current versions of operating system base image and htslib/samtools.

5.1.0 - full collate and samtools markdup

5.1.0

• Base image updated to Focal (Ubuntu 20.04).
• Majority of biobambam2 replaced with samtools functions.
• Reads undergo full collate when mapping from BAM/CRAM (bwa-mem2 prep).
• Duplicate marking samtools markdup --mode options exposed to bwa_mem.pl.
  • Lanes mapped with earlier versions of PCAP-core cannot be merged without reporocessing to add "mate score tag" via samtools fixmate.
• Scramble option for bwa_mem.pl deprecated, relevant option for fast CRAM random access exposed.

5.0.5

noindex option added to merge_or_mark.pl in conjunction with qnamesort option

5.0.4 - Add qnamesort option to merge_or_mark.pl

* Add `qnamesort` connamdline flag to `merge_or_mark.pl` for bammerge…

… calls (Defaults to `SO=coordinate` without)

5.0.2 - use of bwa-mem2 optional

Under 5.0.2 the use of bwa-mem2 is made optional to preserve backward compatibility. If you want this specify the additional parameter -bwamem2 of -bm2.

Please see 5.0.0 release notes for other information about the impact of bwa-mem2.

Please note that at this time bwa-mem2 is considered only a pre release candidate.