I have multiple sequence alignments in Fasta/Clustal format generated from Sanger sequences. I would like to convert them to SAM or BAM files so that I can proceed to variant calling step. Can I know if there is any method or tool to do this ? Thanks.
•
written
by
Louis Kok •
I quickly wrote a tool to convert CLUSTAL to SAM. See https://github.com/lindenb/jvarkit/wiki/Biostar139647
$ curl -sL "https://raw.githubusercontent.com/suryasaha/Pred_cutoff/60a6f980c9940dfb6e381c5394918f27cb14564f/data/Xylella-RpoH.aln" |\
java -jar dist-1.128/biostar139647.jar
@HD VN:1.4 SO:unsorted
@SQ SN:chrUn LN:42
@PG ID:0 VN:3a0c4ccb05e7492382e00328ac60951f215d9400 CL:(empty) PN:Biostar139647
1 0 chrUn 1 60 42M * 0 0 CATACTTGGTCATCGGTCGTGTCCTTGAAAGTGACTTGTTAA *
2 0 chrUn 1 60 42M * 0 0 TCTCTGAACCCCCTTGAAACCCCTACACTCAGCCATATATGC *
3 0 chrUn 1 60 42M * 0 0 TACCTTCGGGTCCTTGAAAATAGCGTCGCCGTGCTTATCTGT *
4 0 chrUn 1 60 5M2D35M * 0 0 TTGACAGCCGCTTGAGCAGGCGTCGGTCATCCCCACATTC *
5 0 chrUn 1 60 18M1D9M1D13M * 0 0 ATGCCTGGGTGGCTTGAAAGCTGGCGGCTTGCCCACATAC *
6 0 chrUn 1 60 20M1D21M * 0 0 TCAGTTTTATCGCTTGATATTCACTGAGACTGGCCACACAT *
Simply awesome. Would it effect SNP calling if we replace the '-' with N's and make 42M for all sequences ?
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Do you have a representative sequence of your MSA which could be used as reference.fasta ? So that SAM header can be created and then sam records.