Questions tagged [samtools]

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,

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7
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7answers
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How to subset a BAM by a list of QNAMEs?

I have a text file 'qnames.txt' with QNAMEs in the following format: EXAMPLE:QNAME1 EXAMPLE:QNAME2 EXAMPLE:QNAME3 EXAMPLE:QNAME4 EXAMPLE:QNAME5 I would like to ...
11
votes
3answers
6k views

Converting a VCF into a FASTA given a reference with Python, R

I am interested in converting a VCF file into a FASTA file given a reference sequence with Python or R. Samtools/BCFtools (Heng Li) provides a Perl script ...
4
votes
1answer
393 views

Error given while trying to index a BAM file with Samtools Index - NO COOR?

I am currently working on my own Metagenomic pipeline, utilizing Bowtie 2 to map. Bowtie 2 outputs a SAM file, which I convert to a .BAM and sort it using Samtools. When I try to utilize Samtools to ...
6
votes
1answer
1k views

Read counts from BAM file

I have few BAM files which are generated from Ion Torrent Server (ampliseq) aligned to hg19 genome. I want to extract read counts from the bam files and I know that "featureCounts" can be used for ...
1
vote
1answer
2k views

Samtools Index: Chromosome Blocks not Continuous

I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai format using ...