What it does

This tool converts a Variant Call Format (VCF) file into a Multiple Alignment Format (MAF) custom track file suitable for display at genome browsers.

This file should be used for display purposes only (e.g as a UCSC Custom Track). Performing an analysis using the output created by this tool as input is not recommended; the source VCF file should be used when performing an analysis.

Unknown nucleotides are represented as '*' as required to allow the display to draw properly; these include e.g. reference bases which appear before a deletion and are not available without querying the original reference sequence.

Example

Starting with a VCF:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA00001 NA00002 NA00003
20  14370   rs6054257   G   A   29  0   NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51  1|0:48:8:51,51  1/1:43:5:-1,-1
20  17330   .   T   A   3   q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50  0|1:3:5:65,3    0/0:41:3:-1,-1
20  1110696 rs6040355   A   G,T 67  0   NS=2;DP=10;AF=0.333,0.667;AA=T;DB   GT:GQ:DP:HQ 1|2:21:6:23,27  2|1:2:0:18,2    2/2:35:4:-1,-1
20  1230237 .   T   .   47  0   NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60  0|0:48:4:51,51  0/0:61:2:-1,-1
20  1234567 microsat1   G   D4,IGA  50  0   NS=3;DP=9;AA=G  GT:GQ:DP    0/1:35:4    0/2:17:2    1/1:40:3

Under the following conditions: VCF Source type: Per Population (file), Name for this population: CHB+JPT Results in the following MAF custom track:

track name="Galaxy Custom Track" visibility=pack
a score=0
s hg18.chr20  14369 1 + 14370 G
s CHB+JPT_1.1     0 1 +     1 A

a score=0
s hg18.chr20  17329 1 + 17330 T
s CHB+JPT_1.2     0 1 +     1 A

a score=0
s hg18.chr20  1110695 1 + 1110696 A
s CHB+JPT_1.3       0 1 +       1 G
s CHB+JPT_2.3       0 1 +       1 T

a score=0
s hg18.chr20  1230236 1 + 1230237 T
s CHB+JPT_1.4       0 1 +       1 .

a score=0
s hg18.chr20  1234565 5 + 1234572 *G--***
s CHB+JPT_1.5       0 1 +       1 *------
s CHB+JPT_2.5       0 7 +       7 *GGA***