Hi,
I have been running to MoDIL to locate indels and have problems interpreting the output. According to the README file
and an excerpt from the predicted INDELs in Yoruban genome from MoDIL website:
I'd interpret the above results as a 75pb insertion starting at pos 218651814 ending at 218652002, and a 329bp deletion from 102759676 to 102760211. I do not understand how an insertion of size 75bp can start at 218651814 and end at 218652002 (i.e., 188 bp apart)? Likewise, in the second line, how a deletion from 102759676 to 102760211 (535 bp in between) can be a 329pb deletion? Could anyone help to explain or to point out what is wrong with my interpretation?
Many thanks
MD
I have been running to MoDIL to locate indels and have problems interpreting the output. According to the README file
Results format is:
- Cluster ID: Unique ID for each indel prediction
- Chromosome: Chromosome where the indel is located.
- Start location: Start location of indel
- End location: End location of indel
- Insertion flag: If it is 1, the row means insertion, deletion otherwise.
- Deletion flag: If it is 1, the row means deletion, insertion otherwise.
- Size of indel: If it is negative it means deletion, insertion otherwise.
(ex) -300 => 300bp deletion
(ex) 12 => 12bp insertion
- P value: P-value of the indel prediction
- Likelihood of homozygosity: If it is homozygous, it is close to 1.
- Number of matepairs that support indel
- Number of matepairs that support no indel: If it is zero, the indel
is homozygous
- Cluster ID: Unique ID for each indel prediction
- Chromosome: Chromosome where the indel is located.
- Start location: Start location of indel
- End location: End location of indel
- Insertion flag: If it is 1, the row means insertion, deletion otherwise.
- Deletion flag: If it is 1, the row means deletion, insertion otherwise.
- Size of indel: If it is negative it means deletion, insertion otherwise.
(ex) -300 => 300bp deletion
(ex) 12 => 12bp insertion
- P value: P-value of the indel prediction
- Likelihood of homozygosity: If it is homozygous, it is close to 1.
- Number of matepairs that support indel
- Number of matepairs that support no indel: If it is zero, the indel
is homozygous
1.0 chr1 218651814 218652002 1 0 75.0 0 1e-09 21220038 0 47 0 25 36 218651906 218651972
1.0 chr1 102759676 102760211 0 1 -329.0 0 1e-09 10323514 0 67 0 32 37 102759712 102760037
1.0 chr1 102759676 102760211 0 1 -329.0 0 1e-09 10323514 0 67 0 32 37 102759712 102760037
Many thanks
MD