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I use the Soapaligner to aligne the sequences ,and change the outfile fomat to sam, but i could use the Soapsnp sofeware base on the aligner result sorted ,and then in IGV to view ,but the sort process has flauts ,i don't konw the reason ,has anyone meet the same problems? thanks! |
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Have you tried sorting the SAM using samtools sort instead of msort? Either there was an error producing the SAM file, or there was a bug in msort. If the SAM file is bad, samtools sort should fail. If the SAM file is okay, samtools sort should turn out just fine. The Picard (Java) implementation of samtools may be easier to install than the C version of samtools. |
Is there a particular fault/error message you get when you try to sort? Are you using soapsnp to sort, or are you using the samtools/Picard binaries?
I use the msort to sort the alignement result ,but the error is "segmentation fault".