Changes

=== Discovery ===

=== Discovery ===

Discovery is performed at per sample level, the evidence sites lists for each sample is then merged and site discovery statistics are computed.

Discovery is performed at per sample level, the evidence sites lists for each sample are then merged and site discovery statistics are computed.

The user then makes a decision on cut offs to make to create an initial site list.

The user then makes a decision on cut offs to make to create an initial candidate site list.

Generates site list with info fields E and N.

Generates site list with info fields E and N.

  vt discover -i NA12878.bam -o NA12878.sites.vcf -g hs37d5.fa

  vt discover -i NA12878.bam -o NA12878.sites.vcf -g hs37d5.fa

Left align variants.

Left align variants.  This is required as left alignment if insertions and/or deletions within a read is sometimes insufficient to ensure complete left alignment.

  vt left_align -i NA12878.bam -o NA12878.leftaligned.sites.vcf -g hs37d5.fa

  vt left_align -i NA12878.bam -o NA12878.leftaligned.sites.vcf -g hs37d5.fa

Evidence site lists are combined across samples and split by sites.

Evidence site lists are combined across samples and split by sites to allow for parallelization.

  vt merge_and_split_sample_vcf -i NA12878.sites.vcf,NA12879.sites.vcf,NA12880.sites.vcf -o 1-1000000.sites.vcf

  vt merge_and_split_sample_vcf -i NA12878.sites.vcf,NA12879.sites.vcf,NA12880.sites.vcf -l 5000

Discovery statistics are computed.

Discovery statistics are computed.  These statistics will allow you to choose a suitable cut off for creating a suitable candidate site list.

  vt compute_discovery_stats -i 1-1000000.sites.vcf -o 1-1000000.annotated.sites.vcf  

  vt compute_discovery_stats -i 1-1000000.sites.vcf -o 1-1000000.annotated.sites.vcf  

A calling pipeline implemented in a make file is available here.

A calling pipeline implemented in a make file is available here.

 

=== Genotyping ===

=== Genotyping ===