for display at UCSCvcf_to_maf_customtrack.py '$out_file1'
#if $vcf_source_type.vcf_file
'${vcf_source_type.vcf_file[0].vcf_input.dbkey}'
#else
'?'
#end if
${vcf_source_type.vcf_source} -n '$track_name'
#for $vcf_repeat in $vcf_source_type.vcf_file
'${vcf_repeat.vcf_input}'
#if $vcf_source_type.vcf_source == '-p'
'${vcf_repeat.population_name}'
#end if
#end for
-g
**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::
##fileformat=VCFv3.3
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000GenomesPilot-NCBI36
##phasing=partial
##INFO=NS,1,Integer,"Number of Samples With Data"
##INFO=DP,1,Integer,"Total Depth"
##INFO=AF,-1,Float,"Allele Frequency"
##INFO=AA,1,String,"Ancestral Allele"
##INFO=DB,0,Flag,"dbSNP membership, build 129"
##INFO=H2,0,Flag,"HapMap2 membership"
##FILTER=q10,"Quality below 10"
##FILTER=s50,"Less than 50% of samples have data"
##FORMAT=GT,1,String,"Genotype"
##FORMAT=GQ,1,Integer,"Genotype Quality"
##FORMAT=DP,1,Integer,"Read Depth"
##FORMAT=HQ,2,Integer,"Haplotype Quality"
#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
##maf version=1
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***