Kun:LabNotes/Haplotyping/2011-9-7

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Haplotyping data analysis

  • Rui&Matt lysed GM12878 cells, and made dilution to ~8 chrosomes per aliquot, then performed tagmentation followed by PCR with indexing primers. Rui prepared 24 libraries (one failed) and Matt prepared 12 libraries (one failed). Each mixture of 12 libraries was sequenced in two lanes (HL101, 60bp+index): Lab notes.

Mapping & variant calling

  • I processed 12 data sets in a batch.
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx1.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx1.txt.gz > s12_Indx1.fq
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx2.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx2.txt.gz > s12_Indx2.fq
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx3.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx3.txt.gz > s12_Indx3.fq
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx4.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx4.txt.gz > s12_Indx4.fq
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx5.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx5.txt.gz > s12_Indx5.fq
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx6.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx6.txt.gz > s12_Indx6.fq
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx7.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx7.txt.gz > s12_Indx7.fq
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx8.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx8.txt.gz > s12_Indx8.fq
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx9.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx9.txt.gz > s12_Indx9.fq
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx10.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx10.txt.gz > s12_Indx10.fq
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx11.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx11.txt.gz > s12_Indx11.fq
  less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx12.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx12.txt.gz > s12_Indx12.fq
  fastq2variants.pl s12_Indx1.fq 60 > s_12_Indx1.log
  fastq2variants.pl s12_Indx2.fq 60 > s_12_Indx2.log
  fastq2variants.pl s12_Indx3.fq 60 > s_12_Indx3.log
  fastq2variants.pl s12_Indx4.fq 60 > s_12_Indx4.log
  fastq2variants.pl s12_Indx5.fq 60 > s_12_Indx5.log
  fastq2variants.pl s12_Indx6.fq 60 > s_12_Indx6.log
  fastq2variants.pl s12_Indx7.fq 60 > s_12_Indx7.log
  fastq2variants.pl s12_Indx8.fq 60 > s_12_Indx8.log
  fastq2variants.pl s12_Indx9.fq 60 > s_12_Indx9.log
  fastq2variants.pl s12_Indx10.fq 60 > s_12_Indx10.log
  fastq2variants.pl s12_Indx11.fq 60 > s_12_Indx11.log
  fastq2variants.pl s12_Indx12.fq 60 > s_12_Indx12.log
  • Then I used samtools to get the read counts for each data set:
 /home/kunzhang/softwares/samtools-0.1.12a/samtools view -c  s12_Indx1.fq.bowtie.sorted.bam
 /home/kunzhang/softwares/samtools-0.1.12a/samtools view -c  s12_Indx1.fq.bowtie.sorted.unique.bam
 Media:Haplotyping_HL101_library_complexity.png
    • We got an average of 3.5 millions reads (median 3.5M) per library, and the average unique reads per library is ~250k (median 117k).
    • With the combination of 34 libraries (equivalent to 6 cells), we have 8.5 millions of unique 60bp reads, which cover 500Mb (or 1/6) of the human genome.
    • If we obtain PE100bp reads, we would cover roughly half of the human genome with the same set of libraries. To obtain 1X coverage of the genome, we need PE100bp reads on ~80 of such libraries.