Zero lifted variants with Picard, CrossMap and bcftools liftover

Question

[Sumaya]

Hi, I am trying to get lifted coordinates of variants for the new hybrid Bos indicus genome assembly (UOA_Brahman_1) using VCF file of variants of Bos taurus genome assembly. I used Picard liftover and CrossMap but both rejected all variants (zero lifted variants). I have tried to change the name of contigs into the one in the chain file but with no avail. I have recently tried Bcftools +liftover plugin as I read that it deals more properly with indels.

Here is the command I ran:

log=${OUP}log/bcflift.log
bcftools +liftover -Oz  -o ${OUP}bcflift/dbSNP150_UOA_lifted.vcf.gz   ${VCF}bos_taurus.dbsnp150_corr.vcf.gz -- \
        -s ${REF}ARS_UCD1.2-cattle/ARS-UCD1.2_Btau5.0.1Y.fa \
        -f ${REF}Bos_indicus_hybrid.UOA_Brahman/Bos_indicus_hybrid.UOA_Brahman_1.dna.toplevel.fa \
        -c ${OUP}bosTau9ToGCF_003369695.1.over.chain.gz \
        --reject  ${OUP}bcflift/dbSNP150_UOA_rejected.vcf.gz \
 2> >(tee -a ${log})

I got this error:

[E::vcf_format] Invalid BCF, CONTIG id=-1 not present in the header
[main_plugin] Error: cannot write to /home/sumaya/liftover_VCFs/bcflift/dbSNP150_UOA_lifted.vcf.gz

Any help will be really appreciated!

Thanks

[Ram]

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