search

mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Other
363 stars 213 forks source link

Genome Build Compatibility Issues #292

Open Jay-Leung opened 2 years ago

Jay-Leung commented 2 years ago

Hi, I am experiencing the same issue as Saya #257

I ran the command:

perl vcf2maf.pl --input-vcf input.vcf --output-maf output.maf --ref-fasta /home/usr/Documents/Genomes/NCBI_RefSeq_GRCh38/GRCh38.p13_RefSeq_NCBI.fa.gz --vep-path ~/ensembl-vep --ncbi-build GRCh38

But I got the same errors:

[W::fai_get_val] Reference chr10:100068503-100068505 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100068503-100068505
[W::fai_get_val] Reference chr10:100220163-100220165 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100220163-100220165
[W::fai_get_val] Reference chr10:100021906-100021908 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100021906-100021908
[W::fai_get_val] Reference chr10:100371703-100371709 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100371703-100371709
[W::fai_get_val] Reference chr10:100167233-100167236 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100167233-100167236
[W::fai_get_val] Reference chr10:100143785-100143787 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100143785-100143787
[W::fai_get_val] Reference chr10:100190058-100190060 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100190058-100190060
[W::fai_get_val] Reference chr10:100184067-100184069 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100184067-100184069
[W::fai_get_val] Reference chr10:100037654-100037656 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100037654-100037656
[W::fai_get_val] Reference chr10:100143654-100143656 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100143654-100143656
[W::fai_get_val] Reference chr10:100360465-100360467 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100360465-100360467
[W::fai_get_val] Reference chr10:100393698-100393700 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100393698-100393700
[W::fai_get_val] Reference chr10:101025788-101025790 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:101025788-101025790
[W::fai_get_val] Reference chr10:100081395-100081397 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100081395-100081397
[W::fai_get_val] Reference chr10:100740777-100740779 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100740777-100740779
[W::fai_get_val] Reference chr10:100128734-100128736 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100128734-100128736
[W::fai_get_val] Reference chr10:100044838-100044840 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100044838-100044840
[W::fai_get_val] Reference chr10:100603389-100603391 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100603389-100603391
[W::fai_get_val] Reference chr10:100290756-100290758 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100290756-100290758
[W::fai_get_val] Reference chr10:100163783-100163785 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100163783-100163785
[W::fai_get_val] Reference chr10:101256069-101256071 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:101256069-101256071
[W::fai_get_val] Reference chr10:100745885-100745887 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100745885-100745887
[W::fai_get_val] Reference chr10:100116219-100116221 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100116219-100116221
[W::fai_get_val] Reference chr10:100220701-100220703 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100220701-100220703
[W::fai_get_val] Reference chr10:100885290-100885292 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100885290-100885292
[W::fai_get_val] Reference chr10:100067861-100067863 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100067861-100067863
[W::fai_get_val] Reference chr10:100424148-100424150 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100424148-100424150
[W::fai_get_val] Reference chr10:100246644-100246646 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100246644-100246646
[W::fai_get_val] Reference chr10:100046765-100046767 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100046765-100046767
[W::fai_get_val] Reference chr10:101316477-101316480 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:101316477-101316480
[W::fai_get_val] Reference chr10:100370242-100370244 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100370242-100370244
[W::fai_get_val] Reference chr10:100291341-100291343 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100291341-100291343
[W::fai_get_val] Reference chr10:100280477-100280479 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100280477-100280479
[W::fai_get_val] Reference chr10:100128762-100128764 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100128762-100128764
[W::fai_get_val] Reference chr10:100246671-100246673 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100246671-100246673
[W::fai_get_val] Reference chr10:100248411-100248413 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100248411-100248413
[W::fai_get_val] Reference chr10:100264594-100264596 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100264594-100264596
[W::fai_get_val] Reference chr10:100220597-100220599 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100220597-100220599
[W::fai_get_val] Reference chr10:100260868-100260870 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100260868-100260870
[W::fai_get_val] Reference chr10:100015853-100015855 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100015853-100015855
[W::fai_get_val] Reference chr10:100625037-100625039 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100625037-100625039
[W::fai_get_val] Reference chr10:100046494-100046496 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100046494-100046496
[W::fai_get_val] Reference chr10:102126600-102126602 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:102126600-102126602
[W::fai_get_val] Reference chr10:100708766-100708768 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100708766-100708768
[W::fai_get_val] Reference chr10:100137176-100137178 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100137176-100137178
[W::fai_get_val] Reference chr10:100194167-100194169 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100194167-100194169
[W::fai_get_val] Reference chr10:100006779-100006781 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100006779-100006781
[W::fai_get_val] Reference chr10:100190036-100190038 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100190036-100190038
[W::fai_get_val] Reference chr10:102155021-102155023 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:102155021-102155023
[W::fai_get_val] Reference chr10:100202454-100202456 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100202454-100202456
[W::fai_get_val] Reference chr10:100694632-100694634 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100694632-100694634
[W::fai_get_val] Reference chr10:100166334-100166336 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100166334-100166336
[W::fai_get_val] Reference chr10:100643924-100643926 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100643924-100643926
[W::fai_get_val] Reference chr10:100991093-100991095 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100991093-100991095
[W::fai_get_val] Reference chr10:100255161-100255163 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100255161-100255163
[W::fai_get_val] Reference chr10:100666657-100666662 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100666657-100666662
[W::fai_get_val] Reference chr10:10075149-10075151 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:10075149-10075151
[W::fai_get_val] Reference chr10:100054044-100054046 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100054044-100054046
[W::fai_get_val] Reference chr10:100258093-100258095 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100258093-100258095
[W::fai_get_val] Reference chr10:100145445-100145447 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100145445-100145447
[W::fai_get_val] Reference chr10:100291533-100291535 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100291533-100291535
[W::fai_get_val] Reference chr10:100385605-100385607 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100385605-100385607
[W::fai_get_val] Reference chr10:100049105-100049107 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100049105-100049107
[W::fai_get_val] Reference chr10:100183965-100183967 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100183965-100183967
[W::fai_get_val] Reference chr10:100268709-100268711 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100268709-100268711
[W::fai_get_val] Reference chr10:100016634-100016636 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100016634-100016636
[W::fai_get_val] Reference chr10:100024771-100024773 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100024771-100024773
[W::fai_get_val] Reference chr10:100389655-100389657 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100389655-100389657
[W::fai_get_val] Reference chr10:100288942-100288944 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100288942-100288944
[W::fai_get_val] Reference chr10:10098771-10098773 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:10098771-10098773
[W::fai_get_val] Reference chr10:100297701-100297717 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100297701-100297717
[W::fai_get_val] Reference chr10:10041250-10041252 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:10041250-10041252
[W::fai_get_val] Reference chr10:100321243-100321245 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100321243-100321245
[W::fai_get_val] Reference chr10:101044758-101044760 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:101044758-101044760
[W::fai_get_val] Reference chr10:100331712-100331717 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100331712-100331717
[W::fai_get_val] Reference chr10:100052544-100052546 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100052544-100052546
[W::fai_get_val] Reference chr10:100194164-100194166 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100194164-100194166
[W::fai_get_val] Reference chr10:101044760-101044762 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:101044760-101044762
[W::fai_get_val] Reference chr10:100289927-100289929 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100289927-100289929
[W::fai_get_val] Reference chr10:100356256-100356258 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100356256-100356258
[W::fai_get_val] Reference chr10:100073691-100073693 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100073691-100073693
[W::fai_get_val] Reference chr10:100144586-100144588 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100144586-100144588
[W::fai_get_val] Reference chr10:100076245-100076247 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100076245-100076247
[W::fai_get_val] Reference chr10:100379559-100379561 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100379559-100379561
[W::fai_get_val] Reference chr10:100097500-100097502 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100097500-100097502
[W::fai_get_val] Reference chr10:100445975-100445977 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100445975-100445977
[W::fai_get_val] Reference chr10:100939605-100939607 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100939605-100939607
[W::fai_get_val] Reference chr10:100417970-100417972 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100417970-100417972
[W::fai_get_val] Reference chr10:100365713-100365715 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100365713-100365715
[W::fai_get_val] Reference chr10:101153780-101153782 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:101153780-101153782
[W::fai_get_val] Reference chr10:100318850-100318852 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100318850-100318852
[W::fai_get_val] Reference chr10:101521918-101521920 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:101521918-101521920
[W::fai_get_val] Reference chr10:102692798-102692800 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:102692798-102692800
[W::fai_get_val] Reference chr10:100167289-100167291 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100167289-100167291
[W::fai_get_val] Reference chr10:100317331-100317334 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100317331-100317334
[W::fai_get_val] Reference chr10:100332859-100332861 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100332859-100332861
[W::fai_get_val] Reference chr10:100690789-100690792 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100690789-100690792
[W::fai_get_val] Reference chr10:100296405-100296407 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100296405-100296407
[W::fai_get_val] Reference chr10:100119928-100119930 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100119928-100119930
[W::fai_get_val] Reference chr10:100145518-100145520 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100145518-100145520
[W::fai_get_val] Reference chr10:100440126-100440128 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100440126-100440128
[W::fai_get_val] Reference chr10:100288757-100288759 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100288757-100288759
[W::fai_get_val] Reference chr10:100619031-100619033 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100619031-100619033
[W::fai_get_val] Reference chr10:100360497-100360499 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100360497-100360499
[W::fai_get_val] Reference chr10:100190019-100190025 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100190019-100190025
[W::fai_get_val] Reference chr10:100616503-100616505 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100616503-100616505
[W::fai_get_val] Reference chr10:100030852-100030854 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100030852-100030854
[W::fai_get_val] Reference chr10:100297247-100297249 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100297247-100297249
[W::fai_get_val] Reference chr10:100600224-100600226 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100600224-100600226
[W::fai_get_val] Reference chr10:100065402-100065404 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100065402-100065404
[W::fai_get_val] Reference chr10:100677788-100677790 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100677788-100677790
[W::fai_get_val] Reference chr10:100297254-100297256 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100297254-100297256
[W::fai_get_val] Reference chr10:100224989-100224991 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100224989-100224991
[W::fai_get_val] Reference chr10:100109937-100109940 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100109937-100109940
[W::fai_get_val] Reference chr10:100023261-100023263 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100023261-100023263
[W::fai_get_val] Reference chr10:100207454-100207456 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100207454-100207456
[W::fai_get_val] Reference chr10:10074957-10074959 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:10074957-10074959
[W::fai_get_val] Reference chr10:100145527-100145529 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100145527-100145529
[W::fai_get_val] Reference chr10:100189673-100189675 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100189673-100189675
[W::fai_get_val] Reference chr10:100136293-100136295 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100136293-100136295
[W::fai_get_val] Reference chr10:100094547-100094550 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100094547-100094550
[W::fai_get_val] Reference chr10:100077498-100077500 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100077498-100077500
[W::fai_get_val] Reference chr10:100719956-100719958 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100719956-100719958
[W::fai_get_val] Reference chr10:100674768-100674771 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100674768-100674771
[W::fai_get_val] Reference chr10:100285898-100285900 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100285898-100285900
[W::fai_get_val] Reference chr10:101285645-101285669 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:101285645-101285669
[W::fai_get_val] Reference chr10:100218125-100218127 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100218125-100218127
[W::fai_get_val] Reference chr10:10110496-10110498 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:10110496-10110498
[W::fai_get_val] Reference chr10:100144148-100144150 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100144148-100144150
[W::fai_get_val] Reference chr10:100114124-100114126 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100114124-100114126
[W::fai_get_val] Reference chr10:100065196-100065198 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100065196-100065198
[W::fai_get_val] Reference chr10:100347493-100347495 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100347493-100347495
[W::fai_get_val] Reference chr10:100233165-100233167 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100233165-100233167
[W::fai_get_val] Reference chr10:100880737-100880742 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100880737-100880742
[W::fai_get_val] Reference chr10:100441793-100441795 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100441793-100441795
[W::fai_get_val] Reference chr10:101198773-101198775 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:101198773-101198775
[W::fai_get_val] Reference chr10:100248725-100248727 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100248725-100248727
[W::fai_get_val] Reference chr10:100343130-100343132 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100343130-100343132
[W::fai_get_val] Reference chr10:100267607-100267609 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100267607-100267609
[W::fai_get_val] Reference chr10:100245545-100245547 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100245545-100245547
[W::fai_get_val] Reference chr10:100120721-100120723 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100120721-100120723
[W::fai_get_val] Reference chr10:100037189-100037191 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100037189-100037191
[W::fai_get_val] Reference chr10:100098177-100098179 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100098177-100098179
[W::fai_get_val] Reference chr10:1000771-1000773 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:1000771-1000773
[W::fai_get_val] Reference chr10:100011684-100011690 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100011684-100011690
[W::fai_get_val] Reference chr10:1006505-1006507 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:1006505-1006507
[W::fai_get_val] Reference chr10:100981914-100981916 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100981914-100981916
[W::fai_get_val] Reference chr10:100356450-100356457 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100356450-100356457
[W::fai_get_val] Reference chr10:100178263-100178265 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100178263-100178265
[W::fai_get_val] Reference chr10:100290589-100290591 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100290589-100290591
[W::fai_get_val] Reference chr10:100746057-100746059 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100746057-100746059
[W::fai_get_val] Reference chr10:10049892-10049894 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:10049892-10049894
[W::fai_get_val] Reference chr10:100247615-100247617 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100247615-100247617
[W::fai_get_val] Reference chr10:100125778-100125780 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100125778-100125780
[W::fai_get_val] Reference chr10:100259199-100259203 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100259199-100259203
[W::fai_get_val] Reference chr10:102536878-102536880 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:102536878-102536880
[W::fai_get_val] Reference chr10:100224880-100224882 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100224880-100224882
[W::fai_get_val] Reference chr10:100738057-100738059 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100738057-100738059
[W::fai_get_val] Reference chr10:100277992-100277994 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100277992-100277994
[W::fai_get_val] Reference chr10:100735527-100735529 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100735527-100735529
[W::fai_get_val] Reference chr10:100128650-100128652 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100128650-100128652
[W::fai_get_val] Reference chr10:100814403-100814405 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100814403-100814405
[W::fai_get_val] Reference chr10:101122878-101122880 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:101122878-101122880
[W::fai_get_val] Reference chr10:100297212-100297214 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100297212-100297214
[W::fai_get_val] Reference chr10:100356553-100356555 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100356553-100356555
[W::fai_get_val] Reference chr10:100256510-100256512 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100256510-100256512
[W::fai_get_val] Reference chr10:100288138-100288140 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100288138-100288140
[W::fai_get_val] Reference chr10:100108691-100108693 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100108691-100108693
[W::fai_get_val] Reference chr10:100421151-100421153 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:100421151-100421153
[W::fai_get_val] Reference chr10:1007009-1007011 not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in chr10:1007009-1007011
ERROR: You're either using an outdated samtools, or --ref-fasta is not the same genome build as your --input-vcf. at vcf2maf.pl line 410.

I have tried with Ensembl's GRCh38 assembly, as well as NCBI RefSeq GRCh38 & GRCh38p13 genome assemblies. Any idea how to resolve this?

Thanks!

ndfriedman commented 2 years ago

In the prior thread cyriac said "The best option for now is to use the official GRCh38 reference FASTA from NCBI". @ckandoth do you mind providing the path to that fasta? Like Jay I have tried downloading a couple different fastas I found online after googling "official GRCh38 reference FASTA from NCBI," but all result in the same 'chr' error

odamame0811 commented 2 years ago

I also have same problem in chr10...

camcecc commented 2 years ago

Same here, I'm getting [faidx] Failed to fetch sequence in chr10 with all downloaded fastas, either NCBI or VEP or USCS

Has someone found a solution??

dining-philosopher commented 1 year ago

Hello!

I overcame this issue by adding chr* definitions to Homo_sapiens.GRCh38.dna.toplevel.fa.gz.fai :

1   248956422   56  60  61
2   242193529   253105808   60  61
3   198295559   499335952   60  61
4   190214555   700936493   60  61
5   181538259   894321347   60  61
6   170805979   1078885300  60  61
7   159345973   1252538102  60  61
8   145138636   1414539898  60  61
9   138394717   1562097568  60  61
10  133797422   1702798922  60  61
11  135086622   1838826360  60  61
12  133275309   1976164484  60  61
13  114364328   2111661107  60  61
14  107043718   2227931566  60  61
15  101991189   2336759404  60  61
16  90338345    2440450504  60  61
17  83257441    2532294546  60  61
18  80373285    2616939669  60  61
19  58617616    2698652566  60  61
20  64444167    2758247200  60  61
21  46709983    2823765494  60  61
22  50818468    2871254034  60  61
X   156040895   2922919533  60  61
Y   57227415    3081561171  60  61
MT  16569   3139742431  60  61
chr1    248956422   56  60  61
chr2    242193529   253105808   60  61
chr3    198295559   499335952   60  61
chr4    190214555   700936493   60  61
chr5    181538259   894321347   60  61
chr6    170805979   1078885300  60  61
chr7    159345973   1252538102  60  61
chr8    145138636   1414539898  60  61
chr9    138394717   1562097568  60  61
chr10   133797422   1702798922  60  61
chr11   135086622   1838826360  60  61
chr12   133275309   1976164484  60  61
chr13   114364328   2111661107  60  61
chr14   107043718   2227931566  60  61
chr15   101991189   2336759404  60  61
chr16   90338345    2440450504  60  61
chr17   83257441    2532294546  60  61
chr18   80373285    2616939669  60  61
chr19   58617616    2698652566  60  61
chr20   64444167    2758247200  60  61
chr21   46709983    2823765494  60  61
chr22   50818468    2871254034  60  61
chrX    156040895   2922919533  60  61
chrY    57227415    3081561171  60  61
chrMT   16569   3139742431  60  61
.....

So my vcf2maf ran perfectly.

dining-philosopher commented 1 year ago

Interestingly this is specifically vcf2maf issue, vep alone runs fine at the same file. Moreover, when i tried to convert such vep output to maf with vcf2maf, it gave me the same error until i applied abovementioned hack.

And by the way, it is not only chr10, when i deleted chr10 variants, it started to curse at chr11.