Are you using the latest version of samtools and HTSlib?
Yes
If not, please specify.
Please describe your environment.
- OS : Linux 4.18.0-553.16.1.el8_10.x86_64
- machine architecture : x86_64
- compiler: gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-22)
Please specify the steps taken to generate the issue, the command you are running and the relevant output.
I want to run markdup -r. In previous versions,
bwa mem -T 50 -Y -M -R '@RG\tID:Sample\tSM:Sample' -t 8 reference.fa R1.fastq.gz R2.fastq.gz | samclip --max 10 --ref reference.fa.fai | samtools sort -n -l 0 --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 --threads 8 -m 1000M | samtools markdup -r -s - - > output.bam
Has worked (samtools v1.20). However, when i try to run the same command with version 1.21 the following errorr is reported
samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.
samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.
I note that in the recent release on https://newreleases.io/project/github/samtools/samtools/release/1.21 the following change has been made to fixmate:
samtools fixmate no longer removes the PAIRED flag from reads that have no mate. This is done on the understanding that the PAIRED flag is a sequencing technology indicator not a feature of alignment. This is a change to previous fixmate behaviour. (PR [#2056](https://github.com/samtools/samtools/pull/2056), fixes [#2052](https://github.com/samtools/samtools/issues/2052). Reported by John Wiedenhoeft)
And i wonder if this has caused my problem. I will rollback to 1.20 for now - but thought it would be nice to get your opinion/advice on this.
Many thanks in advance
Cheers
Kristy
Are you using the latest version of samtools and HTSlib?
Yes
If not, please specify.
Please describe your environment.
Please specify the steps taken to generate the issue, the command you are running and the relevant output.
I want to run
markdup -r. In previous versions,Has worked (samtools v1.20). However, when i try to run the same command with version 1.21 the following errorr is reported
I note that in the recent release on https://newreleases.io/project/github/samtools/samtools/release/1.21 the following change has been made to
fixmate:And i wonder if this has caused my problem. I will rollback to 1.20 for now - but thought it would be nice to get your opinion/advice on this.
Many thanks in advance
Cheers
Kristy