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Shell Programming and Scripting
How do I feed numbers from awk(1) to tail(1)?
Post 302181282 by unilover on Wednesday 2nd of April 2008 02:25:45 PM
04-02-2008
Sorry! "zcat|touch" preou* was in my test!!
You should have "begin|end" mymail.txt
You should have "begin|end" mymail.txt
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LEARN ABOUT DEBIAN
vcf-annotate
VCF-ANNOTATE(1) User Commands VCF-ANNOTATE(1) NAME
vcf-annotate - annotate VCF file, add filters or custom annotations SYNOPSIS
cat in.vcf | vcf-annotate [OPTIONS] > out.vcf DESCRIPTION
About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations. Currently annotates only the INFO column, but it will be extended on demand. OPTIONS
-a, --annotations <file.gz> The tabix indexed file with the annotations: CHR FROM[ TO][ VALUE]+. -c, --columns <list> The list of columns in the annotation file, e.g. CHROM,FROM,TO,-,INFO/STR,INFO/GN. The dash in this example indicates that the third column should be ignored. If TO is not present, it is assumed that TO equals to FROM. -d, --description <file|string> Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'. The descriptions can be read from a file, one annotation per line. -f, --filter <list> Apply filters, list is in the format flt1=value/flt2/flt3=value/etc. -h, -?, --help This help message. Filters: + Apply all filters with default values (can be overridden, see the example below). -X Exclude the filter X 1, StrandBias FLOAT Min P-value for strand bias (given PV4) [0.0001] 2, BaseQualBias FLOAT Min P-value for baseQ bias [1e-100] 3, MapQualBias FLOAT Min P-value for mapQ bias [0] 4, EndDistBias FLOAT Min P-value for end distance bias [0.0001] a, MinAB INT Minimum number of alternate bases [2] c, SnpCluster INT1,INT2 Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases [] D, MaxDP INT Maximum read depth [10000000] d, MinDP INT Minimum read depth [2] q, MinMQ INT Minimum RMS mapping quality for SNPs [10] Q, Qual INT Minimum value of the QUAL field [10] r, RefN Reference base is N [] W, GapWin INT Window size for filtering adjacent gaps [10] w, SnpGap INT SNP within INT bp around a gap to be filtered [10] Example: zcat in.vcf.gz | vcf-annotate -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz zcat in.vcf.gz | vcf-annotate -f +/-a/c=3,10/q=3/d=5/-D -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz Where descriptions.txt contains: key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name' key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand' vcf-annotate 0.1.5 July 2011 VCF-ANNOTATE(1)