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Old 02-17-2012, 02:03 AM   #1
mhadidi2002
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Location: Germany

Join Date: Jun 2011
Posts: 24
Default From bam to wig format

Hello,

I have bam files and I need to convert it to wig format to be like this:

variableStep chrom=chr2
300701 12.5
300702 12.5
300703 12.5
300704 12.5
300705 12.5

I know that there is an options in samtools called: pileup or mpileup, but it doesn't work well with me for the following reason:
if only some nucleotides of a read is mapped to a genome, it reports coverage equally to all nucleotides of that read. I need to report only coverage for mapped nucleotides within the read, do u know any other tool that make this?

Thanks,
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Old 02-17-2012, 03:26 AM   #2
Richard Finney
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Location: bethesda

Join Date: Feb 2009
Posts: 700
Default

Try some thing like this:
samtools depth yourfile.bam | awk '{if ($1!=prev)print "variableStep chrom="$1;print $2"\t"$3;prev=$1}


example :
samtools depth TCGA-23-1110-01A-01W-0486-08_IlluminaGA-DNASeq_capture.bam | awk '{if ($1!=prev)print "variableStep chrom="$1;print $2"\t"$3;prev=$1}' |head
variableStep chrom=chrM
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 2
30 3
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