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Results tagged with samtools
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user 136
Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
2
votes
1
answer
527
views
Samtools sort: most efficient approach to sort a single sample after aligning split .fastq f...
Related to my other question (Samtools sort: most efficient memory and thread settings for many samples on a cluster), we need to optimize samtools sort as we prepare to analyze thousands of .bam files … Is it fastest to:
samtools sort each 'mini-bam' and then samtools merge?
samtools cat the 'mini-bams' together and then samtools sort?
Another option I haven't considered? …
- 1,414
5
votes
2
answers
5k
views
Samtools sort: most efficient memory and thread settings for many samples on a cluster
Complicated question: Has anyone investigated the optimal thread and memory settings to sort hundreds to thousands of .bam files using samtools sort on a cluster? … I'm mostly interested in optimizing samtools sort because the other steps (e.g., alignment) are much more obvious to fine-tune. …
- 1,414
4
votes
1
answer
687
views
BWA mem | samtools view: Intermittent parsing error
I was getting an error from samtools. I should have been able to figure that out, but hopefully this post saves someone else the trouble. … Original post
I'm experiencing a strange intermittent parsing error when piping bwa mem to samtools view. …
- 1,414