Converting to fasta from .bam
Hello,
I haven't found a good reference on how to convert an alignment currently in the .bam format back to .fasta. I was assuming there was a way to do this using Samtools, but I haven't found one. I did see a reference to a Bam2fastq converter, but that is a separate software package.
Thanks very much for any insights you might have.
Zach
1 answer
One easy way is to convert to BED with bam2bed and awk the columns you want into FASTA form:
$ bam2bed < reads.bam | awk '{print ">"$4"\n"$12;}' - > reads.fa
For instance:
$ bam2bed < contigs.bam | awk '{print ">"$4"\n"$12;}' - | head
>Contig545|m.1503
ATGGAGGTGATTGATTTTTCGGAGACGGAGATGGAAGCAGCGGAGCAGCTAGTGCAATTGAGCGAGGATGATACGTTGAGCTGTAGCAGCGGTACAGGCTTGAGCGTTAGCGGTTGTGAAGGCGGATTCCATAGGAAGAGACACAGCGATGTTATTAGTGATGAGGTGCAAAACGACGGCGTTGTACGTACGACGATGAATAACAATGCTACAGACGCTCAATGTTTTGTGAAGGCAATCACGGAGACGAACATAATAAGGAGGAGGTATAAGAAGAAAAAGTTTCGGTCTCTTGCGAGTCTTTACAGGGCAACGAAGGAGATGACGACGGACGAGTTGATCTAG
>Contig1727|m.4383
TTAATCCATTTGTTTCACTTTGTTAGCAGTCTCAATTGGTTTCTTGCTGATCATTTCATGATGGGATATATCTGTGTGGAATCTTTGTTTTGGTTTGACTTTTTGGTCGATGATGATTGACGTTAAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGCCTAAGGCTTTCGCCTTTCGCCGGGCTTGAGAGCTTATGATGTTTTTATCCTTCCTTGGATGTCTGAGACCAAT
>Contig1477|m.3679
TTATAAAAAAGCAATACTATCATGGCGTTGGGGCGAGAAAGAGGCGCAACACATGCCTGTGAGTCCATGACGGCTCCAGAACTCTTCAGTATCAGCGACTCCGTGGATCCTGACTCTTCTCGTGCTCTTCGTGTCTGTGTTGAAGTAGAAAACATAGAAGGGCTGGGCAGGGCCTGGCAGAGATGTTGGGGAGAAAATGATTTCACCGGCCTTGTTGGTTCCTTGGGAGATCATACGCTGACTCCTCCGGAAAGCGAAGGGAAGAGACAAGGAAAGCTGAAATGATTGTCTGGACCACTCATGTTTGGTCACATCCTCCAGTATCCAAAGATCAAAACGGTCGAAAGAAGAACCAGTTCTCAAACAGTTTGTTGGTACAAGGACATCTAGCTTCCCTTTGTATTCTATCAATGATGTATAAACCTTCCAAACCAGGACCTCCTTAGGCGTAGTGATAAAACTTAGTATCCTCTCATATCTTACATCAAAGCACACAAACACAGGAGGAGTTTGATTTGGAACAGAAGCAGCATAATAGATGAAACCATTGATGCTTAGTCCCACAGTCATAGGGCAATAATACGGGGAGGTTCCTTGCGTTTC
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