SwiftLink .dat format

Question

[wanabi]

Hello,

I am planning to do linkage analysis on WES data using SwiftLink(https://github.com/ajm/swiftlink). For this I need three input files: pedigree file, map file and locus data file. Can someone explain me what the format of the later (data file) should be? In the website there is an example file which looks like the one bellow. Can someone please explain me what the meaning of each line is?

Thanks

4 0 0 5
 0 0.0 0.0 0 
 1 2 3 4
1  2    # TRAIT
 0.9999 0.0001
 1
 0.000 0.000 1.000
3  2    # rs1
 0.5000 0.5000
3  2    # rs2
 0.2500 0.7500
3  2    # rs3
 0.3300 0.6700
 0 0
 0.1  0.090635  0.090635
 1      2.0  1.0

Answer 1

[amedlar]

I understand your post is a few months old, but as one of the authors of SwiftLink, I thought I would answer just in case anyone gets here from Google.

SwiftLink uses the standard LINKAGE file formats that several other linkage analysis programs use. The DAT file is defined here in the internet archive copy of the LINKAGE format description. The example you gave (bereft of formatting, see original here) specifies four traits: a disease trait and three SNP markers. The first two lines are program options, the third line states the order of markers, lines 4-7 specify the disease trait including the penetrance function, lines 8-9, 10-11 and 12-13 specify markers labelled rs1, rs2 and rs3, respectively. Lines 14-16 are related to the recombination fractions between markers.

All of these input files are very difficult and tedious to get right by hand, so I strongly recommend people use either Mega2 or Alohomora to generate input files. For both programs you need to generate input files for Allegro (at the time I did not realise there were several, slightly different variants of LINKAGE format).