Changes between Version 9 and Version 10 of SOPs/variant_calling


Ignore:
Timestamp:
03/13/14 10:17:48 (11 years ago)
Author:
gbell
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/variant_calling

    v9 v10  
    6969Annotate variants by adding tags ("filters" but all variants are kept) to each variant, using all default filters.
    7070{{{
    71 bcftools view -L -vcg A_reads.bt2.sorted_unique.raw.bcf | vcf-annotate -f + > A_reads.bt2.sorted_unique.withTags.vcf
     71bcftools view -vcg A_reads.bt2.sorted_unique.raw.bcf | vcf-annotate -f + > A_reads.bt2.sorted_unique.withTags.vcf
    7272}}}
    7373
    … …  
    8383Annotate variants by adding tags, more analysis, and any SNPdb overlaps
    8484{{{
    85 bcftools view -L -vcg A_reads.bt2.sorted_unique.raw.bcf | vcf-annotate -f +/d=10 --fill-HWE --fill-type -n -a SNP137.bed.gz -c CHROM,FROM,TO,INFO/SNP_ID -d key=INFO,ID=SNP_ID,Number=1,Type=Integer,Description='SNP137 sites' > A_reads.bt2.sorted_unique.filtered.vcf
     85bcftools view -vcg A_reads.bt2.sorted_unique.raw.bcf | vcf-annotate -f +/d=10 --fill-HWE --fill-type -n -a SNP137.bed.gz -c CHROM,FROM,TO,INFO/SNP_ID -d key=INFO,ID=SNP_ID,Number=1,Type=Integer,Description='SNP137 sites' > A_reads.bt2.sorted_unique.filtered.vcf
    8686}}}
    8787