User: zengtony743

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zengtony74370
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Canada
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3 years ago
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Posts by zengtony743

<prev • 53 results • page 1 of 6 • next >
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Comment: C: Remove genes that each of a gene with multiple SNVs
... Thanks Alex, this is the first time to use vcf2bed, When i run $ perl PATH/vcf2bed.pl —keep-header < my_file.vcf It shows Cannot open --keep-header at PATH/vcf2bed.pl line 12 my_file.vcf works fine, did I miss something? ...
written 3.2 years ago by zengtony74370
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Remove a gene with multiple variants after snpEff annotation (VCF file)
... Here is an example of the information of the VCF data line: chr10 4450587 . T C 2757.97 PASS ANN=C|downstream_gene_va riant|MODIFIER|Armt1|ENSMUSG00000061759|transcript|ENSMUST00000143037.6|processe d_transcript||n.*175T>C|||||175|,C|intron_variant|MODIFIER|Armt1|ENSMUSG00000061 ...
vcf filter multiple variants in one gene written 3.3 years ago by zengtony74370
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Comment: C: Remove genes that each of a gene with multiple SNVs
... Thanks ! Just don't know what's going on with my cell phone today ...
written 3.3 years ago by zengtony74370
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Remove genes that each of a gene with multiple SNVs
... I generated a vcf file with snpEff annotation tool . In this file, there are many genes needed to be removed because a gene with multiple SNVs, these are all false positive SNVs that I need to remove. Is there tools can do this? I usually do manually by transferring vcf to a txt format file and then ...
vcf written 3.3 years ago by zengtony74370 • updated 3.3 years ago by Alex Reynolds29k
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Comment: C: snpEff mouse annotation failed because of computer resource limitation?
... Thanks genomax2 . That is weird. I use a snpEff package via a public open resource from my working place. Now I have to download it and run it under my account seeing how it goes ...
written 3.3 years ago by zengtony74370
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snpEff mouse annotation failed because of computer resource limitation?
... I set the amount of memory in java virtual machine from 4G to 75G... it just failed. $ java -Xmx75G -jar path/snpEff/4.11/snpEff.jar GRCm38.71 myfile.vcf > myfile.ann.vcf & $ java.lang.RuntimeException: java.lang.RuntimeException: Cannot create directory '/hpf/tools/centos6/snpEff ...
annotation snpeff mouse written 3.3 years ago by zengtony74370
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a running error when running vcf-isec
... 1) shared SNPs in all three samples $ vcf-isec -n +3 4751_97PASS.vcf.gz 4751_42PASS.vcf.gz 4751PASS.vcf.gz | gzip -c > 4751shared.vcf.gz & 2)Error $ Leading or trailing space in attr_key-attr_value pairs is discouraged: [Description] [DP < 5 ] FILTER= at /hpf/tool ...
vcf-isec written 3.3 years ago by zengtony74370 • updated 3.3 years ago by Zev.Kronenberg11k
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Comment: C: select Het variants from VCF
... Sorry for the typo. I mean it should be "4751_42R" but not "4751_42R” the keyboard for the new Macbook is so confusing ...
written 3.3 years ago by zengtony74370
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Answer: A: select Het variants from VCF
... finally figured it out... because of "4751_42R” should be "4751_42" ...
written 3.3 years ago by zengtony74370
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select Het variants from VCF
... I am trying to select heterozygotes from the VCF file. having been using this command many times and it works all the time. But something error pops up this time, do not know what is the problem. 1) partial data line information is like this CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 4751 ...
heterozygotes selectvariant error written 3.3 years ago by zengtony74370

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