What Should Be Specified For The "--Mates_File_Ref" Parameter In The Sv Detect Tool?

Question

[vishal.rossi]

Sv Detect cnv asks for following things :

http://svdetect.sourceforge.net/Site/Manual.html

- 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

Answer 1

[Istvan Albert]

As it says in the manual you wil need to provide the mate-pair alignment file in sam format.

Saying it doesn't work is not meaningful without specifying in what way does it not work.

Perhaps your SAM file is does not have anything that could be detected.

Answer 2

[seidel]

The documentation is confusing and incomplete. To compare two BAM (or SAM) files using the cnv command, you have to specify both of them in the configuration file, and in different sections. In the "general" section you place the path to the bam file for the sample of interest ("mates_file", what will be the value for the numerator of the resulting ratios), and in the "detection" section you place the path for the reference bam ("mates_file_ref", what will be the value of the denominator) to which the sample will be compared. The result should be a text file with log ratios of the sample to the reference. If you get an error, pay attention to it and try moving things around (or report it specifically).