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% VCFLENGTH(1) vcflength (vcflib) | vcflength (VCF transformation) % Erik Garrison and vcflib contributors

NAME

vcflength

SYNOPSIS

vcflength

DESCRIPTION

Add length info field

EXAMPLES


Example:

**vcflength** samples/sample.vcf
##fileformat=VCFv4.0
(...)
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001 NA00002 NA00003
19      111     .       A       C       9.6     .       length=0;length.alt=1;length.ref=1      GT:HQ   0|0:10,10  0|0:10,10       0/1:3,3
19      112     .       A       G       10      .       length=0;length.alt=1;length.ref=1      GT:HQ   0|0:10,10  0|0:10,10       0/1:3,3
20      14370   rs6054257       G       A       29      PASS    AF=0.5;DP=14;NS=3;length=0;length.alt=1;length.ref=1;DB;H2 GT:GQ:DP:HQ     0|0:48:1:51,51  1|0:48:8:51,51  1/1:43:5:.,.
20      17330   .       T       A       3       q10     AF=0.017;DP=11;NS=3;length=0;length.alt=1;length.ref=1     GT:GQ:DP:HQ     0|0:49:3:58,50  0|1:3:5:65,3    0/0:41:3:.,.
20      1110696 rs6040355       A       G,T     67      PASS    AA=T;AF=0.333,0.667;DP=10;NS=2;length=0,0;length.alt=1,1;length.ref=1;DB   GT:GQ:DP:HQ     1|2:21:6:23,27  2|1:2:0:18,2    2/2:35:4:.,.
20      1230237 .       T       .       47      PASS    AA=T;DP=13;NS=3;length=0;length.alt=1;length.ref=1GT:GQ:DP:HQ      0|0:54:.:56,60  0|0:48:4:51,51  0/0:61:2:.,.
20      1234567 microsat1       G       GA,GAC  50      PASS    AA=G;AC=3,1;AN=6;DP=9;NS=3;length=1,2;length.alt=2,3;length.ref=1  GT:GQ:DP        0/1:.:4 0/2:17:2        1/1:40:3
20      1235237 .       T       .       0       .       length=0;length.alt=1;length.ref=1      GT      0/00|0     ./.
X       10      rsTest  AC      A,ATG   10      PASS    length=-1,1;length.alt=1,3;length.ref=2 GT      0 0/1      0|2

Type: transformation

EXIT VALUES

0 : Success

not 0 : Failure

SEE ALSO

vcflib(1)

OTHER

Source code

vcflength.cpp

LICENSE

Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.