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Revision as of 12:11, 19 August 2015

650 bytes added ,  12:11, 19 August 2015
→‎Discover2
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=== Discover2 ===
 
=== Discover2 ===
   −
Discovers variants from reads in a BAM or CRAM file.
+
Discovers variants from reads in a BAM/CRAM file.
    
<div class=" mw-collapsible mw-collapsed">
 
<div class=" mw-collapsible mw-collapsed">
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   vt discover -b NA12878.bam -s NA12878 -r hs37d5.fa -i 20 -v snps,indels,mnps
 
   vt discover -b NA12878.bam -s NA12878 -r hs37d5.fa -i 20 -v snps,indels,mnps
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
  usage : vt discover [options]  
+
usage : vt discover2 [options]  
   −
  options : -b  input BAM file
+
options : -b  input BAM/CRAM file
−
            -v  variant types [snps,mnps,indels]
+
          -y  soft clipped unique sequences cutoff [0]
−
            -f  fractional evidence cutoff for candidate allele [0.1]
+
          -x  soft clipped mean quality cutoff [0]
−
            -e  evidence count cutoff for candidate allele [2]
+
          -w  insertion desired type II error [0.0]
−
            -q  base quality cutoff for bases [13]
+
          -c  insertion desired type I error [0.0]
−
            -m MAPQ cutoff for alignments [20]
+
          -h  insertion fractional evidence cutoff [0]
−
            -s  sample ID
+
          -g  insertion count cutoff [1]
−
            -r  reference sequence fasta file []
+
          -n  deletion desired type II error [0.0]
−
            -o  output VCF file [-]
+
          -m  deletion desired type I error [0.0]
−
            -I  file containing list of intervals []
+
          -v  deletion fractional evidence cutoff [0]
−
            -i  intervals []
+
          -u  deletion count cutoff [1]
−
            --  ignores the rest of the labeled arguments following this flag
+
          -k  snp desired type II error [0.0]
−
            -h displays help
+
          -j  snp desired type I error [0.0]
 +
          -f  snp fractional evidence cutoff [0]
 +
          -e  snp evidence count cutoff [1]
 +
          -q  base quality cutoff for bases [0]
 +
          -C  likelihood ratio cutoff [0]
 +
          -B  reference bias [0]
 +
          -a  read exclude flag [0x0704]
 +
          -l  ignore overlapping reads [false]
 +
          -t MAPQ cutoff for alignments [0]
 +
          -p  ploidy [2]
 +
          -s  sample ID
 +
          -r  reference sequence fasta file []
 +
          -o  output VCF file [-]
 +
          -z  ignore MD tags [0]
 +
          -d  debug [0]
 +
          -I  file containing list of intervals []
 +
          -i  intervals []
 +
          -? displays help
    
  </div>
 
  </div>
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