lobSTR seems to mis-genotype reads (or at least some reads) where the STR (in this case, a poly-G region) has an N in the middle. Is there any way to fix/change this behavior?
Example:
The following read was put into lobSTR (STR bold):
TCTCGGCATCAACATCCAGAGTTTAGGGACCATGTCCCAGTCTCTGTGAGGTGGATGGGAAGTCAACATTAGTTGACTGAGCACCACCTGCGTGGAAGATGCAGCCCCCCCCNGCCCCATCACTGGGAATACAGTGCTGAGCAGGACAGCACCTGATGTGCGAGGGGGAAGACAGACAACAAATACATAAGCAATGGAATGTACCTTTGGCAGGCCGAT
The tags attached to the read by lobSTR afterwards are:
XS:i:46990694
XE:i:46990706
XR:Z:C
XD:i:-5
XC:f:13
XG:Z:CCCCCCC
XX:i:1
XM:i:-1
XQ:i:41
RG:Z:lobSTR;s66;spike_in
NM:i:7
I believe this to be incorrectly genotyped, as the tags should be:
XS:i:46990694
XE:i:46990706
XR:Z:C
XD:i:1
XC:f:13
XG:Z:CCCCCCCCNGCCCC
...
Is there an easy way to fix this behavior?
As a note, we can't use HipSTR for this application because we want a genotype per read, and HipSTR does not allow us to get the level of detail we need for our studies (effectively, pooled populations of cells with unknown population size).
Brendan
lobSTR seems to mis-genotype reads (or at least some reads) where the STR (in this case, a poly-G region) has an N in the middle. Is there any way to fix/change this behavior?
Example:
The following read was put into lobSTR (STR bold):
TCTCGGCATCAACATCCAGAGTTTAGGGACCATGTCCCAGTCTCTGTGAGGTGGATGGGAAGTCAACATTAGTTGACTGAGCACCACCTGCGTGGAAGATGCAGCCCCCCCCNGCCCCATCACTGGGAATACAGTGCTGAGCAGGACAGCACCTGATGTGCGAGGGGGAAGACAGACAACAAATACATAAGCAATGGAATGTACCTTTGGCAGGCCGAT
The tags attached to the read by lobSTR afterwards are:
XS:i:46990694
XE:i:46990706
XR:Z:C
XD:i:-5
XC:f:13
XG:Z:CCCCCCC
XX:i:1
XM:i:-1
XQ:i:41
RG:Z:lobSTR;s66;spike_in
NM:i:7
I believe this to be incorrectly genotyped, as the tags should be:
XS:i:46990694
XE:i:46990706
XR:Z:C
XD:i:1
XC:f:13
XG:Z:CCCCCCCCNGCCCC
...
Is there an easy way to fix this behavior?
As a note, we can't use HipSTR for this application because we want a genotype per read, and HipSTR does not allow us to get the level of detail we need for our studies (effectively, pooled populations of cells with unknown population size).
Brendan