Kun:LabNotes/Haplotyping/2011-6-14

From ZhangLabWiki
Jump to navigation Jump to search

Generate the GM12878 reference haplotypes[edit]

  • 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[edit]

  • 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.
  nohup fastq2variants.pl s_4_Indx1.txt 80 > s_4_Indx1.log &
  • Compare the alleles called from each file with the GM12878 reference haplotype using pileupVsRefHap.pl
  ./pileupVsRefHap.pl s_4_Indx1.bowtie.pileup > s_4_Indx1.idioGraph.txt &
 File:370858186TASK04720.png
 File:460858749TASK04721.png
 File:12085989TASK04722.png
 File:180859144TASK04723.png
 File:240859843TASK04724.png
 File:290859775TASK04725.png
 File:350859778TASK04726.png
 File:400859757TASK04727.png
 File:460859626TASK04728.png
 File:530859451TASK04729.png
 File:580859248TASK04730.png
 File:040900426TASK04731.png