sinamajidian
commented
2 weeks ago - Looks like a heterozygous deletion in Tumor (but not in Normal)
- In Tumor, the coverage of PacBio in neighboring area is ~50 and ~23 in the deletion part.
- In hifiasm assembly, there is a deletion only in hap2 not in hap1.
- Clear breakpoints as reported.
- In ONT, there is one read suggesting longer deletion (792bp) and another read suggesting shorter (783bp).
- In both ONT/PacBio there are a small portion of reads without deletion, so it could be sub-clonal.
- The coverage of a position in the middle of deletion is half of neighboring
- Break points look good
chr13 84309984 Minda_37 N <DEL> . PASS SVLEN=788;SVTYPE=DEL;SUPP_VEC=PB_ID_14112_2,PB_d_83,ONT_ID_58187_2,ONT_d_43,ILL_MantaDEL:205694:0:1:0:0:0,PB_severus_DEL1823,ONT_severus_DEL2014,PB_Sniffles2.DEL.1ACMC,ONT_Sniffles2.DEL.1EBMC,ILL_900253031:2,ILL_gridss216fb_6871hhttps://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr13:84309984#ribbon