Probably one of the most freq FAQ
latest thread in biostar
http://biostar.stackexchange.com/questions/6993/convert-bam-file-to-fasta-file
Samtofastq using Picard
http://picard.sourceforge.net/command-line-overview.shtml#SamToFastq
Samtools and awk to make fasta from sam
latest thread in biostar
http://biostar.stackexchange.com/questions/6993/convert-bam-file-to-fasta-file
Samtofastq using Picard
http://picard.sourceforge.net/command-line-overview.shtml#SamToFastq
Samtools and awk to make fasta from sam
samtools view filename.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' - > filename.fasta Biopython and pysam (code contributed by Brad Chapman)http://biostar.stackexchange.com/questions/6993/convert-bam-file-to-fasta-file/6994#6994 
What about the calmd option? Sequences are full of '=' signs, will cause your awk script to fail; will some of the other tools handle it? Which?
ReplyDeleteMaybe one should add that (at least with bwa) it is possible to do alignment drectly from BAM files without the need to convert to FastQ, which might be space-consuming...
ReplyDelete