Hello Saurav Saha, Although the UCSC Genome Browser has the ability to display SAM/BAM tracks, we are not qualified to answer questions regarding the use of the samtools programs. Please direct your question to the samtools help desk here: http://sourceforge.net/mail/?group_id=246254
You may want to let them know about this line of your file: tail -n +851271 input.sam | head -1 They will also probably want to know which tool generated the SAM. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu ----- Original Message ----- From: "saurav saha" <[email protected]> To: [email protected] Sent: Wednesday, February 3, 2010 11:03:02 PM GMT -08:00 US/Canada Pacific Subject: [Genome] samtools issue Dear All, I am using samtools for sam to bam conversion. but when i used view command along with -b -h -S -t -o parameters, initially it starts but it midst of conversion it gets aborted. and it shows: [sam_header_read2] 1 sequences loaded. Parse error at line 851271: mapped sequence without CIGAR Can anybody tell me what exactly is the problem and any other converter which can solve this problem? NOTE: I have already checked my SAM file on IGV and it is showing the alignment. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
