select only deletions in vcf file

Question

[alexmondaini]

Apparently the Broad Institute discourages people from writing their own scripts/parsers for vcf files. https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format , quoting from the link:

"No, really, do not write your own parser if you can avoid it. This is not a comment on how smart or how competent we think you are -- it is a comment on how annoyingly obtuse and convoluted the VCF format is. "

So I've used their own gatk tools to select variants of my interest, problem is to filter only for INDELS my vcf output remains with insertions, and I want only deletions.

This is my GATK command:

gatk SelectVariants -V ~{vcf} -O ~{output_vcf} --select-type-to-include INDEL

Does anyone know other tools that may select only for deletion or is gatk capable of doing that ? I read the tool documentation and apparently it cannot perform this task.

Answer 1

[Pierre Lindenbaum]

using vcffilterjdk: http://lindenb.github.io/jvarkit/VcfFilterJdk.html

java -jar ${JVARKIT_DIST}/vcffilterjdk.jar -e 'return variant.getAlternateAlleles().stream().filter(A->!A.isSymbolic()).anyMatch(A->A.length()< variant.getReference().length());'  ./test/resources/rotavirus_rf.vcf.gz

(...)
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
RF02    1962    .   TACA    TA  33.43   .   AC=1;AN=10;DP=43;DP4=22,11,2,0;HOB=0.02;ICB=0.0439024;IDV=3;IMF=0.3;INDEL;MQ=60;MQ0F=0;MQSB=1;SGB=0.810227;VDB=0.373246
RF04    1259    .   ATTT    ATT 41.02   .   AC=1;AN=10;DP=39;DP4=8,6,2,1;HOB=0.02;ICB=0.0439024;IDV=6;IMF=1;INDEL;MQ=60;MQ0F=0;MQSB=1;SGB=2.33665;VDB=0.869183
RF04    1857    .   CAGA    CA  39.47   .   AC=1;AN=10;DP=45;DP4=12,21,1,1;HOB=0.02;ICB=0.0439024;IDV=2;IMF=0.166667;INDEL;MQ=60;MQ0F=0;MQSB=1;SGB=0.810227;VDB=0.969947
RF06    1129    .   ATTT    AT  78  .   AC=2;AN=10;DP=31;DP4=0,20,0,5;HOB=0.32;ICB=0.425;IDV=5;IMF=0.833333;INDEL;MQ=60;MQ0F=0;SGB=5.5074;VDB=0.344193
RF11    74  .   CAAAAA  CAA 113 .   AC=1;AN=10;DP=82;DP4=55,0,5,0;HOB=0.02;ICB=0.0439024;IDV=7;IMF=0.388889;INDEL;MQ=60;MQ0F=0;SGB=5.5074;VDB=0.00911888
(...)