BOL: Wire posts tagged with 'Bam'

Wire post by Shruti Paniwala

Shruti Paniwala — Thu, 23 Jun 2016 09:00:18 -0500

#Extract #tabbed info from #BAM file with samtools: samtools view test.bam|awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $4+length($10)-1}' > file.xls

Surabhi Chaudhary — Wed, 23 Mar 2016 05:48:58 -0500

#BAM file to #fastaq #conversion with #Samtool: samtools view filename.bam | awk '{OFS="\t"; print "@"$1"\n"$10"\n+\n"$11}' >| filename.fastq

Surabhi Chaudhary — Wed, 23 Mar 2016 05:47:41 -0500

#BAM file to fasta #conversion with #Samtool: samtools view filename.bam | \
awk '{OFS="\t"; print ">"$1"\n"$10}' - > filename.fasta

Rahul Agarwal — Sun, 30 Nov 2014 14:59:03 -0600

http://bam.iobio.io/ #bam #vcf #analysis

Jit — Fri, 23 May 2014 10:11:28 -0500

Extract list of read ID from bam file: samtools view mbi.sorted.bam |perl -ne '/ID/ && print' > extractedID.sam #Extract #Ids #SAM #BAM #NGS