Question: no successful variants lifted over from hs37d5_plusRibo_plusOncoViruses_plusERCC.fa to GRCh38
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gravatar for jing.mengrabbit
3 months ago by
jing.mengrabbit10 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 • 254 views
ADD COMMENTlink modified 6 days ago by tiwari.tanushree0 • written 3 months ago by jing.mengrabbit10

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

ADD REPLYlink written 3 months ago by rbagnall1.3k

Yes, they have different chromosome names.

ADD REPLYlink written 3 months ago by jing.mengrabbit10

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 9 days ago by tiwari.tanushree0

Please see here

ADD REPLYlink modified 6 days ago by RamRS18k • written 9 days ago by jing.mengrabbit10

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 6 days ago by tiwari.tanushree0
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