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Results tagged with samtools
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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
How to convert a Pileup file to VCF format with Hg19 alignment
Commonly used tools for variant calling include samtools, GATK, and FreeBayes.
Long answer
Converting data files from one format to another is a common task in bioinformatics. …
- 5,110
1
vote
Accepted
Control width of samtools tview "snapshot" when redirecting
I cross-posted this question on the official samtools issue tracker, and finally got a response.
Looking at the code for the HTML view, I see this and this. … So maybe try
COLUMNS=200 samtools tview -d H -p CHR:X-Y aln.bam ref.fasta …
- 5,110
6
votes
Frequency of specific viral sequence in .BAM or .fastq
Most read aligners will report unaligned reads as well, which presumably will include your viral sequences. I would ask them to formally confirm that the BAM files will contain unaligned reads before …
- 5,110