I am trying to get a count of all bases, insertions and deletions from a bam file viewed in IGV genome viewer for each individual nucleotide. I can get the counts for the bases as a wig file (example shown below):
track type=wiggle_0
#Columns: Pos, Combined Strands A, Combined Strands C, Combined Strands G, Combined Strands T, Combined Strands N
variableStep chrom=E17F span=1
1 0 241 0 0 0
2 337 0 0 0 0
3 414 0 1 1 0
4 6 412 8 5 0
5 4 411 30 5 0
6 475 6 2 0 0
7 9 1 417 69 0
However, I also really want to get the count of deletions for each position. It is possible to get this count if you go through each position individually and write down the numbers (as shown in the image). But I was thinking surely there must be a way to do this in IGV? I have tried igvtools but it still doesn't give me a deletion count. Any guidance or other suggestions will be greatly appreciated!
Thanks
-T
track type=wiggle_0
#Columns: Pos, Combined Strands A, Combined Strands C, Combined Strands G, Combined Strands T, Combined Strands N
variableStep chrom=E17F span=1
1 0 241 0 0 0
2 337 0 0 0 0
3 414 0 1 1 0
4 6 412 8 5 0
5 4 411 30 5 0
6 475 6 2 0 0
7 9 1 417 69 0
However, I also really want to get the count of deletions for each position. It is possible to get this count if you go through each position individually and write down the numbers (as shown in the image). But I was thinking surely there must be a way to do this in IGV? I have tried igvtools but it still doesn't give me a deletion count. Any guidance or other suggestions will be greatly appreciated!
Thanks
-T
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