Assembly convertor errors

Question

[caro-ca]

Hi, all! I used the sacCer2 genome assembly (for S. cerevisiae) to call variants, but now I want to map the coordinates of the variants in the VCF file to another genome assembly (sacCer3). I used two web interface software: Lift Genome Annotations and Ensembl Assembly Converter

Lift Genome Annotation raised an error of: Unsupported data format. However, I used a BED file that looks like this:

chrI    22231   22232   INS00BED        .       N       <INS>   PASS    SUPP=30;SUPP_VEC=001000001001010001000110000000000010111000001000100001001111000011100110101011000010001000010;SVLEN=320;SVTYPE=I>
chrI    29149   29150   INS00BED        .       N       <INS>   PASS    SUPP=5;SUPP_VEC=000000000010000001001000000000000000000000000000000000000000000000000000000000000010000001000;SVLEN=0;SVTYPE=INS;>

For Ensembl Assembly Converter I got retrieved an incomplete VCF file:

##fileformat=VCFv4.1
##source=SURVIVOR
##fileDate=20200816
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=BND,Description="Translocation">
##ALT=<ID=INS,Description="Insertion">
##INFO=<ID=CIEND,Number=2,Type=String,Description="PE confidence="" interval="" around="" END"="">
##INFO=<ID=CIPOS,Number=2,Type=String,Description="PE confidence="" interval="" around="" POS"="">
##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for="" END="" coordinate="" in="" case="" of="" a="" translocation"="">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position="" of="" the="" structural="" variant"="">
##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping="" quality="" of="" paired-ends"="">
##INFO=<ID=RE,Number=1,Type=Integer,Description="read support"="">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural="" variation"="">
##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural="" variation"="">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of="" the="" SV"="">
##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Method for="" generating="" this="" merged="" VCF="" file."="">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of="" the="" SV."="">
##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="Vector of="" supporting="" samples."="">
##INFO=<ID=SUPP,Number=1,Type=String,Description="Number of="" samples="" supporting="" the="" variant"="">
##INFO=<ID=STRANDS,Number=1,Type=String,Description="Indicating the="" direction="" of="" the="" reads="" with="" respect="" to="" the="" type="" and="" breakpoint."="">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PSV,Number=1,Type=String,Description="Previous support="" vector"="">
##FORMAT=<ID=LN,Number=1,Type=Integer,Description="predicted length"="">
##FORMAT=<ID=DR,Number=2,Type=Integer,Description="# supporting="" reference,variant="" reads="" in="" that="" order"="">
##FORMAT=<ID=ST,Number=1,Type=String,Description="Strand of="" SVs"="">
##FORMAT=<ID=QV,Number=1,Type=String,Description="Quality values:="" if="" not="" defined="" a="" .="" otherwise="" the="" reported="" value."="">
##FORMAT=<ID=TY,Number=1,Type=String,Description="Types">
##FORMAT=<ID=ID,Number=1,Type=String,Description="Variant ID="" from="" input."="">
##FORMAT=<ID=RAL,Number=1,Type=String,Description="Reference allele="" sequence="" reported="" from="" input."="">
##FORMAT=<ID=AAL,Number=1,Type=String,Description="Alternative allele="" sequence="" reported="" from="" input."="">
##FORMAT=<ID=CO,Number=1,Type=String,Description="Coordinates">
##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)
##liftOverFile=/net/isilonP/public/ro/ensweb-data/latest/tools/www/e101/assembly_converter/saccharomyces_cerevisiae/EF2_to_R64-1-1.chain.gz
##new_reference_genome=/net/isilonP/public/ro/ensweb-data/latest/tools/www/e101/assembly_converter/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa
##liftOverTime=September06,2020
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample  Sample_1        Sample_2        Sample_3        Sample_4        Sample_5        Sample_6        Sample_7        Sample_8
        Sample_9        Sample_10       Sample_11       Sample_12       Sample_13       Sample_14       Sample_15       Sample_16       Sample_17       Sample_18       Sample_19       Sample_20       Sample_21       Sample_22       Sample_23       Sample_24       Sample_25       Sample_26       Sample_27       Sample_28       Sample_29       Sample_30       Sample_31       Sample_32       Sample_33
       Sample_34       Sample_35       Sample_36       Sample_37       Sample_38       Sample_39       Sample_40       Sample_41       Sample_42       Sample_43       Sample_44       Sample_45       Sample_46       Sample_47       Sample_48       Sample_49       Sample_50       Sample_51       Sample_52       Sample_53       Sample_54       Sample_55       Sample_56       Sample_57       Sample_58
       Sample_59       Sample_60       Sample_61       Sample_62       Sample_63       Sample_64       Sample_65       Sample_66       Sample_67       Sample_68       Sample_69       Sample_70       Sample_71       Sample_72       Sample_73       Sample_74       Sample_75       Sample_76       Sample_77       Sample_78       Sample_79       Sample_80       Sample_81       Sample_82       Sample_83
       Sample_84       Sample_85       Sample_86       Sample_87       Sample_88       Sample_89       Sample_90       Sample_91       Sample_92
73R46UzIr2tCYmGG (1).vcf (END)

I hope you could tell me the error. Thank you in advance.

Answer 1

[GenoMax]

Perhaps crossmap (LINK) will work.

[caro-ca]

Great!! Thank you so much!! It worked!!