Dear ANGSD team,
I am trying to create a consensus sequence from a BAM file using ANGSD. Since my sample is ancient, I would like to remove transitions from the output. I am able to run the -doFasta 2 command with -rmTrans 0 successfully. However, the program always segfaults when I run with -rmTrans 1. This it the command:
angsd -minQ 30 -setMinDepth 2 -i file.bam -doFasta 2 -doCounts 1 -rmTrans 1 -ref genomeRef.fasta -out test.consensus.fasta -nThreads 10
I have also tried running with the -r flag to split the regions under analysis, and it works only when I limit the region to a maximum of 40,000 bp. I have checked the BAM file and it appears to be fine.
Do you have any idea why this is happening or how I might work around it?
Thank you very much for your help.
Dear ANGSD team,
I am trying to create a consensus sequence from a BAM file using ANGSD. Since my sample is ancient, I would like to remove transitions from the output. I am able to run the -doFasta 2 command with -rmTrans 0 successfully. However, the program always segfaults when I run with -rmTrans 1. This it the command:
angsd -minQ 30 -setMinDepth 2 -i file.bam -doFasta 2 -doCounts 1 -rmTrans 1 -ref genomeRef.fasta -out test.consensus.fasta -nThreads 10
I have also tried running with the -r flag to split the regions under analysis, and it works only when I limit the region to a maximum of 40,000 bp. I have checked the BAM file and it appears to be fine.
Do you have any idea why this is happening or how I might work around it?
Thank you very much for your help.