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Old 02-09-2017, 07:33 AM   #1
tristan dubos
Location: France

Join Date: Dec 2015
Posts: 39
Default Problem igvtools count

Hi ,

I would like to detect some genome position indel. So i decide to use igvtools count to extract details for all position sequenced in my 900 dataset. I used for every amplicon this command :

bash igvtools count --query=chr1:162741785-162741920 --strands read -w 1 --bases data_sorted.bam positions_amplicon.wig hg19.fa
I got this kind of result ( output file positions_amplicon.wig) :
track type=wiggle_0
#Columns: Pos, Positive Strand A, Positive Strand C, Positive Strand G, Positive Strand T, Positive Strand N, Positive Strand DEL, Positive Strand INS, Negative Strand A, Negative Strand C, Negative Strand G, Negative Strand T, Negative Strand N, Negative Strand DEL, Negative Strand INS
variableStep chrom=chr1 span=1
162741785 2638.0 0.0 1.0 0.0 0.0 0.0 0.0 2535.0 0.0 3.0 0.0 0.0 0.0 0.0
162741786 0.0 2640.0 0.0 0.0 0.0 0.0 7.0 0.0 2540.0 0.0 0.0 0.0 0.0 0.0

Problem : for my 92 amplicon i test in 900 dataset (add by genomic position ) i found the last columns always equal to 0 , that mean Negative Strand INS never appends in my reads alignments. I check some data with igv graphic and there is Negative Strand INS in some position.

Is my command wrong ? or is there some bug in igvtools ?

Best regards ,

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