Page Comparison

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Based on the discussion above, we are selecting the first solution and providing details of how this command should be run. As this command will generate very little output and take ~45 minutes to complete, you are once again reminded that the output file from this option is in $BI/ngs_course/human_variation as all.samtools.vcf if you want to work with it without having to wait on the analysis to run personally.

mkdir $SCRATCH/GVA_Human_trios/multi_sample
cd $SCRATCH/GVA_Human_trios
samtools mpileup -uf $SCRATCH/GVA_Human_trios/raw_files/ref/hs37d5.fa \
  $SCRATCH/GVA_Human_trios/raw_files/NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam \
  $SCRATCH/GVA_Human_trios/raw_files/NA12891.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam \
  $SCRATCH/GVA_Human_trios/raw_files/NA12892.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam \
    | bcftools call -v -c - > multi_sample/trios_tutorial.all.samtools.vcf

This command again will generate very little output and take ~10 minutes to complete. The observant students who start this command might notice that this time mpileup does give a message that it is working with 3 samples, and 3 input files (while all previous analysis have used 1 file and 1 sample).

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     3435 0/1	0/1	0/0
     20 0/10	0/01	0/10
     2018 0/01	0/10	0/01
     14 0/1	1/1	0/0
      6 0/0	0/1	0/1
      45 1/1	1/1	0/0
      1 1/1	0/1	0/0
      1 0/1	0/0	0/0

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     3435 0/1	0/1	0/0
     20 0/1	0/0	 0/1 0/0
     2018 0/01	0/10	0/01
     14 0/1	1/1	0/0	# middle can't be child
      6 0/0	0/1	0/1
      45 1/1	1/1	0/0	* No mendelian combination exists
      1 1/1	0/1	0/0	*
      1 0/1	0/0	0/0	*

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