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marufdu07 02-05-2012 06:12 PM

how to convert SAM file to BED or MUT
Hi all, I am PhD 1st year student, Now working with the high thoughput sequencing data file to search SNPs. I am working with SAM extension file of Chromosome 1 by using IGV 2.0 software. Can anyone give some idea how to convert SAM file to MUT or BED file? I am not sure whether there is any way or not. Regards, Maruf

mgogol 02-06-2012 06:36 AM

samtools to go from sam to bam, bedtools bamToBed to go from bam to bed.

marufdu07 02-07-2012 03:20 AM

Hi mgogol,
Thanks for your reply.
where I can get the sam tools or bedtools? How about MUT files?

As mentioned earlier I am IGV 2.0, I tried by using RUN igvtools. I could convert SAM to tdf /idx/sai extension files only.

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