but you're using END as the position of the translocation for CHR2 citing John Marshall 's answer: https://www.biostars.org/p/386345/#386354 , this usage of END breaks the integrity of the tabix index , the variant is not found anymore with bcftools or tabix:
Moving this issue from macarthur-lab/gnomad_browser#140. Originally opened by @lindenb.
Cross posted at https://www.biostars.org/p/386345/
What you did: I downloaded the SV from gnomad:
there is a translocation at: 12 :60718971
but you're using END as the position of the translocation for CHR2 citing John Marshall 's answer: https://www.biostars.org/p/386345/#386354 , this usage of END breaks the integrity of the tabix index , the variant is not found anymore with bcftools or tabix:
@jmarshall commented:
Dropping the grep from this last query highlights the unfortunate state that this corrupt index is in: