User: mab658

gravatar for mab658
mab65820
Reputation:
20
Status:
New User
Location:
Last seen:
2 months, 2 weeks ago
Joined:
3 months, 4 weeks ago
Email:
m*****@cornell.edu

Posts by mab658

<prev • 17 results • page 1 of 2 • next >
0
votes
1
answer
1.4k
views
1
answers
Comment: C: How to combine chromosome vcf files
... Hi Pierre, I wanted to merge VCF files which had already splitted by chromosones into a single file. Though each is compressed i.e. chr1.vcf.gz, chr2.vcf.gz, ......chrn.vcf.gz. I could not see any an output file merged.vcf.gz when I used the command. Is it because the file is compressed? java ...
written 10 weeks ago by mab65820
0
votes
1
answer
1.1k
views
1
answers
Comment: C: Calculate mean_GQ value from individual GQ values in a multi-sample VCF file
... This is what I have been looking for. I applied it to my work and it went well. I have chrom, pos, and sample with their respective GQ values. How do I get the average across all the samples for each site (i.e chrom and pos). I need the average so that I can plot it in R. ...
written 3 months ago by mab65820
0
votes
0
answers
240
views
0
answers
Comment: C: how to generate genetic maps from VCF snps data
... I am using beagle 5.0 program for imputation. ...
written 3 months ago by mab65820
0
votes
0
answers
240
views
0
answers
how to generate genetic maps from VCF snps data
... Hi Everyone, Could someone guide me on how to generate genetic map from snps VCF file in order to use it for imputation. I have filtered my snps VCF file and I need genetic map for the imputation. I got to know that one can use PLINK. I need to know what I need to extract from my data prior to us ...
snp sequencing written 3 months ago by mab65820
4
votes
1
answer
205
views
1
answer
why filtering sites with allele count below 3
... Hi everyone, I came across SNP filtering tutorial where the author used the flag `--mac 3` to filter SNPs that have a minor allele count less than 3. That is `vcftools --vcf input_file.vcf --mac 3 --recode --out filtered_file` Could someone explain to me why filtering out sites with minor allele ...
snp sequencing written 3 months ago by mab65820 • updated 3 months ago by Jean-Karim Heriche18k
0
votes
4
answers
12k
views
4
answers
Comment: C: How to filter vcf file on minimum genotype depth and quality for each sample
... from the above script, --minGQ and --minDP take the value of 15 and 10 respectively for filtering genotype quality and depth. Is there any criteria for choosing 15 and 10.. Just to know if 15 and 10 are standard values to use for those flags. ...
written 3 months ago by mab65820
1
vote
2
answers
386
views
2
answers
Conversion of imputed VCF file to HapMap format
... Hi Everyone, I have successfully imputed my VCF file using beagle4.1. How do I convert it to HapMap format, please? Thanks. ...
rna-seq snp written 3 months ago by mab65820 • updated 3 months ago by 159932162500
0
votes
2
answers
2.6k
views
2
answers
Comment: C: Filtering of low coverage variants from VCF
... Dear All, I am having similar problem in determining the appropriate filtering criteria for the snps depth and quality. I am just a beginner in using `vcftools` for snps call filtering.How do i translate the hard filters below using vcftools: that is QualByDepth (QD) 2.0 FisherStrand (FS) 60.0 RMSMa ...
written 3 months ago by mab65820
0
votes
1
answer
392
views
1
answers
Comment: C: Imputation of vcf file
... Thanks Kevin. Your response has been very helpful! Prior to imputation, I cleaned my VCF file using `vcftools` --gzvcf snps.vcf.gz --maf 0.01 --max-missing 0.8 --min-meanDP 10 --recode --out snp_filtered.vcf.gz Please how do I filter 'junk' variants that have a high statistical probability of bein ...
written 3 months ago by mab65820
0
votes
1
answer
392
views
1
answers
Comment: C: Imputation of vcf file
... After imputation using beagle 4.1, I have output with genotypes phased like 0|0, 0|1, etc as follows: ##fileformat=VCFv4.2 ##filedate=20181226 ##source="beagle.27Jul16.86a.jar (version 4.1)" ##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= ##FORMAT= ##FORMAT= #C ...
written 3 months ago by mab65820 • updated 3 months ago by Kevin Blighe41k

Latest awards to mab658

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1204 users visited in the last hour