Can maf2vcf handle hg38 maf as input ? #162
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Same errors no matter what genome build I use: hg19 maf download from https://portal.gdc.cancer.gov/legacy-archive/files/b2e25bdf-f2b5-4a37-b330-05251ea09f2c hg38 maf download from https://portal.gdc.cancer.gov/files/0458c57f-316c-4a7c-9294-ccd11c97c2f9 Please help me. |
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I try using UCSC $ ../biotools/vcf2maf/maf2vcf.pl --input-maf ~/Downloads/gsc_LUAD_pairs.aggregated.capture.tcga.uuid.automated.somatic.maf --output-dir ./test_vcfs --ref-fasta ~/Annotation/reference/hg19.fa
[W::fai_fetch] Reference 19:58420782-58420784 not found in FASTA file, returning empty sequence
Failed to fetch sequence in 19:58420782-58420784
[W::fai_fetch] Reference 10:26581394-26581396 not found in FASTA file, returning empty sequence
Failed to fetch sequence in 10:26581394-26581396
[W::fai_fetch] Reference 14:20528636-20528638 not found in FASTA file, returning empty sequence
Failed to fetch sequence in 14:20528636-20528638
[W::fai_fetch] Reference 11:55657434-55657436 not found in FASTA file, returning empty sequence
Failed to fetch sequence in 11:55657434-55657436
[W::fai_fetch] Reference 1:78269058-78269060 not found in FASTA file, returning empty sequence
Failed to fetch sequence in 1:78269058-78269060
ERROR: Make sure that ref-fasta is the same genome build as your MAF: /home/diviner-wsx/Annotation/reference/hg19.fa
$ ../biotools/vcf2maf/maf2vcf.pl --input-maf ../data/TCGA.LUAD.mutect.hg38.somatic.maf --output-dir ./test_vcfs --ref-fasta ~/Annotation/reference/hg38.fa
$ cd test_vcfs/
$ ls -lh
total 1.8G
-rw-rw-r-- 1 diviner-wsx diviner-wsx 33K 3月 28 18:14 TCGA.LUAD.mutect.hg38.somatic.pairs.tsv
-rw-rw-r-- 1 diviner-wsx diviner-wsx 1.8G 3月 28 18:17 TCGA.LUAD.mutect.hg38.somatic.vcf
Thank your tool, the hg38 works. So the hg19 geome build TCGA used is neither equals to ensembl v75 or UCSC hg19? |
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But the conent of vcf is very weird. 😢 How to explain this???
Left is outcome and the right is normal vcf file. I open it using notepad++,
It seems normal, I am not sure. What the right part means? |
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@ShixiangWang there are many different files and commands you're using here. There is only one rule for maf2vcf - the |
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Thanks, I will write a script to check the output.
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在 2018年3月28日，下午10:13，Cyriac Kandoth <notifications@github.com<mailto:notifications@github.com>> 写道：
@ShixiangWang<https://github.com/ShixiangWang> there are many different files and commands you're using here. There is only one rule for maf2vcf - the --ref-fasta chromosome names and lengths must exactly match the chromosomes used in the --input-maf.
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It is most likely that your |
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@ckandoth Yes, the While Neither Should I use GRCh 37.p13 Thank you very much, |
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The error |
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@ckandoth Thanks for your help. |
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Hi,
I want to transform hg38 maf to vcf,
I know how to download the file, but the info remind me using GRCh37 while maf file I use based on hg38. Can I use this command, or I should use hg19 maf file?
Best wishes,
Shixiang
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