search

cgroza / GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
Other
121 stars 6 forks source link

prepTSD filters #22

Closed cgroza closed 8 months ago

cgroza commented 8 months ago

In line 24 of prepTSD, we explicitly filter VCF records by presence of "DEL" and "INS".

awk '/n_hits=1/ && /INS/ {print $1"\t"$2"\t"($2)+1"\t"$3; next} /n_hits=1/ && /DEL/ {print $1"\t"$2"\t"($2+length($4))"\t"$3; next} /n_hits=2/ && /INS/ && /5P_INV/ {print $1"\t"$2"\t"($2)+1"\t"$3; next} /n_hits=2/ && /DEL/ && /5P_INV/ {print $1"\t"$2"\t"($2+length($4))"\t"$3}' > oneHit_SV_coordinates.bed

This works with VCFs created by GraffiTE, but VCFs from other sources may not be annotated quite the same way. For example, the HPRC VCFs are annotated with "del" and "ins". Therefore, a more general approach is necessary to filter deletions and insertions. Perhaps with bcftools and its ILEN field.