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

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

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.