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Thread | Thread Starter | Forum | Replies | Last Post |
Is it possible to convert a SNP.txt to a bed file or get a SNP.bed from samtools? | Ling | Bioinformatics | 7 | 04-02-2015 07:17 AM |
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#1 |
Junior Member
Location: Japan Join Date: Feb 2012
Posts: 3
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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
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#2 |
Senior Member
Location: Kansas City Join Date: Mar 2008
Posts: 197
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samtools to go from sam to bam, bedtools bamToBed to go from bam to bed.
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#3 |
Junior Member
Location: Japan Join Date: Feb 2012
Posts: 3
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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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