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samtools mpileup -uf $BI/ref_genome/fasta/ucsc/ucsc.hg19.fasta \ $BI/ngs_course/human_variation/NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam \ | bcftools view -vcg - > test.raw.vcf |
or via qsub:
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launcher_creator.py -n samtools_test -b "samtools mpileup -uf ref/hs37d5.fa NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | bcftools view -vcg - > test.raw.vcf" -t 01:00:00 -q development -a CCBB -m samtools qsub samtools_test.sge |
Note that the reference chosen for mpileup must be exactly the same as the reference used to create the bam file. The 1000 genomes project has created it's own reference and so the command listed above won't work - we have to use the 1000 genomes reference which is $BI/ngs_course/human_variation/ref/hs37d5.fa. We could have chosen another mapper if we'd wanted to though.
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