Daniel:Notebook/Haplotyping/2014-1-22: Difference between revisions

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and the PGP1F data, specifically the variant calls from the data from the published paper (Ball et al, PNAS 2005):
and the PGP1F data, specifically the variant calls from the data from the published paper (Ball et al, PNAS 2005):
  [http://www.personalgenomes.org/data/PGP12.05/ PGP1F data]
  [http://www.personalgenomes.org/data/PGP12.05/ PGP1F data]
==Converting Variant Call File==
The variant calls from Ball et al were originally in a .tsv in the format provided by complete genomics.  Most programs use a vcf file so I used a [http://www.completegenomics.com/analysis-tools/toolrepository/masterVarformattoVCFformatfileconverter/ converter], found on the Complete Genomics website, to change the file to the more widely used format.
'''Convert .tsv to .vcf'''
./masterVar2VCFv41 var-GS00253-DNA_D02_200_37-ASM.tsv genome.fa.bz2 pgp1f_hg19_vcf.vcf
This should have yielded a .vcf file which tells all of the possible variants at an SNP given the reference genome from hg19.
==Novoalign==
'''Mask SNPs using the .vcf file'''
novoutil iupac pgp1f_hg19_vcf.vcf genome.fa > hg19_genome_vcfmasked.fa

Latest revision as of 19:03, 22 January 2014

HiC Data Analysis[edit]

Back to Calendar

From the data from Bing Ren's lab, I'm planning on working through the HaploSeq analysis pipeline.

Input Data[edit]

The HiC data from Bing Ren's lab can be found on Genome Miner at:

/home/kunzhang/seqStore/140110_HiC_BingRen

Also being used are the hg19 whole genome fasta file:

/GenomeDB/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa

and the PGP1F data, specifically the variant calls from the data from the published paper (Ball et al, PNAS 2005):

PGP1F data

Converting Variant Call File[edit]

The variant calls from Ball et al were originally in a .tsv in the format provided by complete genomics. Most programs use a vcf file so I used a converter, found on the Complete Genomics website, to change the file to the more widely used format.

Convert .tsv to .vcf

./masterVar2VCFv41 var-GS00253-DNA_D02_200_37-ASM.tsv genome.fa.bz2 pgp1f_hg19_vcf.vcf

This should have yielded a .vcf file which tells all of the possible variants at an SNP given the reference genome from hg19.

Novoalign[edit]

Mask SNPs using the .vcf file

novoutil iupac pgp1f_hg19_vcf.vcf genome.fa > hg19_genome_vcfmasked.fa