Sv Detect cnv asks for following things :
1- Calculation of depth-of-coverage log-ratios
>> SVDetect cnv -conf <configuration_file>
a- Usage parameters in the <detection> block:
-- split_mate_file (m)
Flag to split the original mate file per chromosome for parallel computing
-boolean, value= 1 (run), 0 (skip - already done)
-- window_size(m)
size of the sliding-window used for partioning the genome in bp
-integer, ex: 30000
-- step_length(m)
length of the sliding-window step in bp, set this parameter to get overlapped windows
-integer, ex: 10000
--mates_file_ref(m)
full path to the normal mate-pair input data file of the reference
-text, ex: /align/bowtie/reference_norm_mates.sam
I have problem with mates_file_ref. I put the full mapped sam file of the sample, it doesn't work. the Human reference Genome human_g1k_v37_Ensembl_MT_66.fasta doesn't work (it shouldn't work ideally).
Does anyone has any idea which file path should I provide there.
Thanks in advance
1- Calculation of depth-of-coverage log-ratios
>> SVDetect cnv -conf <configuration_file>
a- Usage parameters in the <detection> block:
-- split_mate_file (m)
Flag to split the original mate file per chromosome for parallel computing
-boolean, value= 1 (run), 0 (skip - already done)
-- window_size(m)
size of the sliding-window used for partioning the genome in bp
-integer, ex: 30000
-- step_length(m)
length of the sliding-window step in bp, set this parameter to get overlapped windows
-integer, ex: 10000
--mates_file_ref(m)
full path to the normal mate-pair input data file of the reference
-text, ex: /align/bowtie/reference_norm_mates.sam
I have problem with mates_file_ref. I put the full mapped sam file of the sample, it doesn't work. the Human reference Genome human_g1k_v37_Ensembl_MT_66.fasta doesn't work (it shouldn't work ideally).
Does anyone has any idea which file path should I provide there.
Thanks in advance