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i am using samtools view option to convert sam2bam (sam file generated using novoalign version 2.05.17) but am getting an error. [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort! can someone help? the aim is to sort the bam file and then call snps/indels using maq |
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thanks qtrinh. i did that but am getting a segmentaton fault. [sam_header_read2] 28406716 sequences loaded. Segmentation fault Guys, this new format, if you're commenting on an answer, please use the "comment" button --->
(21 May '10, 12:05)
ECO ♦♦
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novoalign -o SAM should create the @SQ records but if you use native format and then novo2sam.pl there will be no @SQ records. Try running novoalign -o SAM with just a few reads and then take the SAM header records from this file and add them to the file from novo2sam.pl |
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Hi Bin, The poster was asking about samtools view and sam data built with novo2sam.pl, so I was suggesting a method to get the @SQ records into the SAM file. Aside from that I prefer samtools to maq because it was designed to handle indels in consensus and snp calling, while maq adds indels on as an after thought. You also have a selection of realigners (GATK & DNAA) that can help resolve consensus sequence around indels in sam alignments. I avoid using any aligners, snp callers, viewers etc. that don't handle indels. @DNAA - you're thinking about SRMA (http://srma.sf.net). I am the author of both :)
(15 Jun '10, 13:25)
nilshomer
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