Changes between Version 22 and Version 23 of SOPs/variant_calling


Ignore:
Timestamp:
08/22/17 09:16:53 (8 years ago)
Author:
gbell
Comment:

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Legend:

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  • SOPs/variant_calling

    v22 v23  
    7777Annotate variants by adding tags ("filters" but all variants are kept) to each variant, using all default filters.
    7878{{{
    79 bcftools view -vcg A_reads.bt2.sorted_unique.raw.bcf | vcf-annotate -f + > A_reads.bt2.sorted_unique.withTags.vcf
     79bcftools view A_reads.bt2.sorted_unique.raw.bcf | vcf-annotate -f + > A_reads.bt2.sorted_unique.withTags.vcf
    8080}}}
    8181
    … …  
    9191Annotate variants by adding tags, more analysis, and any SNPdb overlaps
    9292{{{
    93 bcftools 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
     93bcftools view 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
    9494}}}
    9595