Visualizing Snps In Multiple Samples On A Given Gene

Question

[tommivat]

I am working with collections of human exome sequences and developing an interactive UI for browsing interesting SNP (indel and SV) data on samples. My current challenge is to provide per-gene-visualizations for given samples. One purpose of the visualization is to easily provide quick look on how similar / different genetic variation is between the samples in a given gene. The visualization should contain at least the following:

1) overview of chromosomal region with important sites, such as TFBS, TSS and exomes marked,

2) different transcripts, and

3) SNPs for the selected samples.

I realize that this kind of tool might not exist at all. In that case, are there any online genome viewers, in which you can easily provide additional sites to show (in this case the SNPs). I can provide the SNP information in either rsid, location of .vcf format.

Answer 1

[Pierre Lindenbaum]

My variation-toolkit contains a tool named "ucscgeneps". It reads a tab-delimited file CHROM/POS/(SAMPLE), sends a mysql query to the UCSC database and displays the genes as a Postscript file:

$ cat sample2vcf.tsv | tr -d ' ' |\
  scanvcf |\
  awk -F '      ' '($3==".")' |\
  normalizechrom |\
  sort -t '  ' -k1,1 -k2,2n -k11,11 |\
  head -n 10000 |\
  ucscgenesps  -s 11 > result.ps

[tommivat]

Thanks Pierre! This is pretty close what I'm looking for.