Question: no successful variants lifted over from hs37d5_plusRibo_plusOncoViruses_plusERCC.fa to GRCh38
1
gravatar for jing.mengrabbit
15 months ago by
jing.mengrabbit30 wrote:

I ran picard LiftoverVcf to lift over a VCF file from hs37d5_plusRibo_plusOncoViruses_plusERCC.fa to GRCh38 with chain file hg19ToHg38.over.chain, but no successful variants are lifted over. The following is the output:

INFO 2018-07-19 11:30:39 LiftoverVcf Loading up the target reference genome.

INFO 2018-07-19 11:30:48 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.)

INFO 2018-07-19 11:30:51 LiftoverVcf Processed 35989 variants.

INFO 2018-07-19 11:30:51 LiftoverVcf 35989 variants failed to liftover.
INFO 2018-07-19 11:30:51 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over.
INFO 2018-07-19 11:30:51 LiftoverVcf 100.0000% of variants were not successfully lifted over and written to the output.

INFO 2018-07-19 11:30:51 LiftoverVcf liftover success by source contig:

INFO 2018-07-19 11:30:51 LiftoverVcf 1: 0 / 1797 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 10: 0 / 1105 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 11: 0 / 1119 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 12: 0 / 1963 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 13: 0 / 1564 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 14: 0 / 775 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 15: 0 / 675 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 16: 0 / 888 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 17: 0 / 895 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 18: 0 / 650 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 19: 0 / 800 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 2: 0 / 3578 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 20: 0 / 903 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 21: 0 / 619 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 22: 0 / 433 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 3: 0 / 2993 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 4: 0 / 3207 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 5: 0 / 1460 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 6: 0 / 2549 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 7: 0 / 2372 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 8: 0 / 2642 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf 9: 0 / 1426 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf X: 0 / 1570 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf Y: 0 / 6 (0.0000%)

INFO 2018-07-19 11:30:51 LiftoverVcf lifted variants by target contig:

INFO 2018-07-19 11:30:51 LiftoverVcf no successfully lifted variants

WARNING 2018-07-19 11:30:51 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats.

INFO 2018-07-19 11:30:51 LiftoverVcf Writing out sorted records to final VCF.

Can you please help me with this problem? Thank you.

assembly • 894 views
ADD COMMENTlink modified 12 months ago by tiwari.tanushree0 • written 15 months ago by jing.mengrabbit30

Do the chromosome names in hs37d5 look like 1, 2, 3 etc, and in GRCh38 look like chr1, chr2, chr3?

ADD REPLYlink written 15 months ago by rbagnall1.4k

Yes, they have different chromosome names.

ADD REPLYlink written 15 months ago by jing.mengrabbit30

What can be done if the chromosome names are different? I am also facing the same problem as jing, Any help or suggestions? Thank you

ADD REPLYlink written 12 months ago by tiwari.tanushree0

Please see here

ADD REPLYlink modified 12 months ago by RamRS24k • written 12 months ago by jing.mengrabbit30

I have made chain file myself using UCSC tool, It is non-human species and it has different notations for chromosomes. ANy suggestions.

With Regards, Tanushree

ADD REPLYlink written 12 months ago by tiwari.tanushree0
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