Kun:LabNotes/Haplotyping/2011-6-14

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Generate the GM12878 reference haplotypes

  • Download the variant files for GM12878, GM12891(father), GM12892(mother) from Complete Genomics' ftp site:
  ftp://ftp2.completegenomics.com/Pedigree_1463/ASM_Build36_1.10.0/
  GS12878-1100-36-ASM-VAR-files.tar
  GS12891-1100-36-ASM-VAR-files.tar
  GS12892-1100-36-ASM-VAR-files.tar
  
  In Unix, you can use wget to download files:
  wget ftp://ftp2.completegenomics.com/Pedigree_1463/ASM_Build36_1.10.0/NA12878/GS12878-1100-36-ASM-VAR-files.tar
  tar -xvf GS12878-1100-36-ASM-VAR-files.tar
  tar -xvf GS12891-1100-36-ASM-VAR-files.tar
  tar -xvf GS12892-1100-36-ASM-VAR-files.tar
  Find the dbSNPAnnotated files, uncompress them
  bzip2 -d dbSNPAnnotated-GS12878-1100-36-ASM.tsv.bz2
  bzip2 -d dbSNPAnnotated-GS12891-1100-36-ASM.tsv.bz2
  bzip2 -d dbSNPAnnotated-GS12892-1100-36-ASM.tsv.bz2
  trioVar2hap.pl dbSNPAnnotated-GS12878-1100-36-ASM.tsv dbSNPAnnotated-GS12891-1100-36-ASM.tsv dbSNPAnnotated-GS12892-1100-36-ASM.tsv > GM12878_hap.txt

Analysis of HL095 data

  • The experiment was performed by Rui.
    • Dilution of 5-cell lysate to ~1pg per reaction;
    • Tagmentation;
    • PCR with barcodes;
    • Pooled and sequencing in one lane, obtained SE80bp reads.
  • Call variants from each of the 12 files with fastq2variants.pl.
  • Compare the alleles called from each file with the GM12878 reference haplotype.
  • Visualize the parental alleles with Idiographica.
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