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Revision as of 09:08, 1 July 2014
, 09:08, 1 July 2014→Annotating Variants with EPACTS
mkdir --p $OUT/assoc
mkdir --p $OUT/assoc
$EPACTS/bin/epacts-anno --in $OUT/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz --out $OUT/assoc/snps.anno.vcf.gz
$EPACTS/bin/epacts-anno --in $OUT/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz --out $OUT/assoc/snps.anno.vcf.gz --ref $SS/ref22/human.g1k.v37.chr22.fa
Then you will see a series of messages before annotation finishes.
Then you will see a series of messages before annotation finishes.
<div class="mw-collapsible-content" style="width:800px">
<div class="mw-collapsible-content" style="width:800px">
/home/hmkang/seqshop/epacts/bin/anno -i /net/seqshop-server/hmkang/out/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz -r \
/home/hmkang/seqshop/epacts/bin/anno -i /net/seqshop-server/hmkang/out/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz -r \
/home/hmkang/seqshop/epacts/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/hmkang/seqshop/epacts/share/EPACTS/hg19_gencodeV14.txt.gz \
/home/hmkang/seqshop/ref22/human_g1k_v37.chr22.fa -f refGene -g /home/hmkang/seqshop/epacts/share/EPACTS/hg19_gencodeV14.txt.gz \
-c /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt -o /net/seqshop-server/hmkang/out/assoc/snps.anno.vcf.gz --inputFormat vcf \
-c /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt -o /net/seqshop-server/hmkang/out/assoc/snps.anno.vcf.gz --inputFormat vcf \
-p /home/hmkang/seqshop/epacts/share/EPACTS/priority.txt
-p /home/hmkang/seqshop/epacts/share/EPACTS/priority.txt
Gene Annotation
Gene Annotation
Parameters : -g [/home/hmkang/seqshop/epacts/share/EPACTS/hg19_gencodeV14.txt.gz]
Parameters : -g [/home/hmkang/seqshop/epacts/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/hmkang/seqshop/epacts/share/EPACTS/human_g1k_v37.fasta]
-r [/home/hmkang/seqshop/ref22/human_g1k_v37.chr22.fa]
--inputFormat [vcf], --checkReference, -f [refGene]
--inputFormat [vcf], --checkReference, -f [refGene]
-p [/home/hmkang/seqshop/epacts/share/EPACTS/priority.txt]
-p [/home/hmkang/seqshop/epacts/share/EPACTS/priority.txt]
-u [], -d [], --se [], --si [], --outputFormat []
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/hmkang/seqshop/epacts/share/EPACTS/human_g1k_v37.fasta...
Load reference genome /home/hmkang/seqshop/ref22/human_g1k_v37.chr22.fa...
DONE: 84 chromosomes and 3101804739 bases are loaded.
DONE: 1 chromosomes and 51304566 bases are loaded.
Load codon file /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt...
Load codon file /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt...
DONE: codon file loaded.
DONE: codon file loaded.
