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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,
1
vote
How to extract all sequences mapped to a transcript from Kallisto output
Alternatively, you could also just convert the bam to sam and then look for lines where the 3rd field (the reference the sequence is aligned to) is what you want:
samtools view pseudoalignments.bam | awk …
- 10.6k
4
votes
Get a certain gene sequence from bam/vcf and reference
The first approach that comes to mind is to cut the bam file and then convert the already cut bam to fasta:
samtools view -hb chr1:10100500-10200500 > small.bam
samtools fasta small.bam > small.fa
(note … that I am not certain about the samtools fasta command, I have never used it and I don't know if it will produce many sequences, one for each haplotype supported by reads; please test this.) …
- 10.6k
1
vote
Detect mutation context in a read of a sam file
If you want to look at a few, specific reads manually, you can do this on VarSome. We have recently released a new feature that allows you to enter single NGS or Sanger reads and get the list of varia …
- 10.6k
3
votes
Running bwa mem and samtools in one script on a linux cluster
So you would want a loop like this (I removed the unnecessary samtools view step, since samtools sort can handle the sam to bam conversion, and the also unnecessary -r option; if you know you need the … sample_name=${file%_1*}
file2=${file/_1/_2}
mkdir -p "$outBamsDir"/"$sample_name"
bwa mem \
-t 14 \
/path/to/contig/contigs.fasta \
"$file" "$file2" |
samtools …
- 10.6k
1
vote
Accepted
How to reverse complement the DNA sequences for given inverse/reverse coordinates?
The exonerate tool comes with some very handy utilities for sequence manipulation. Here, we are interested in fastasubseq and fasterevcomp. First, install exonerate as described here. If you're using …
- 10.6k
5
votes
Accepted
Aligning FASTQs to FASTA reference
samtools view -bS $STUDY-data.sam > $STUDY-data.bam
This simply converts the SAM file to a BAM file. Essentially a compressed SAM. … samtools view -b -f 12 -F 256 $STUDY-data.bam > $STUDY-data-no-human.bam
Here, you are filtering your bam. …
- 10.6k
1
vote
Error while calling bcftools mpileup - Failed to open -: unknown file type
The - is usually used to mean standard input when reading data. So the message would suggest that the second bcftools command fails to read from stdin, so it fails to read the output of the first bcft …
- 10.6k