Question

I merged 2 VCF files using bcftools, however how should I update the fields according to 2 VCF files

score 48 · Answer 1 · 2024-03-08T14:46:45.760000

48

Views

I merged 2 VCF files using bcftools, however how should I update the fields according to 2 VCF files

Published on 08 March 2024 at 14:46

score 17 · Answer 2 · 2024-03-07T11:51:10.610000

17

Views

Filtering VCF files with bcftools

Published on 07 March 2024 at 11:51

score 22 · Answer 3 · 2024-03-07T04:29:10.233000

22

Views

Separating alleles for 'bcftools merge' when ploidy >2

Published on 07 March 2024 at 04:29

score 14 · Answer 4 · 2024-02-25T03:33:17.053000

14

Views

How to extract all variant alleles that do not match "./." from the GT column of a vcf file?

Published on 25 February 2024 at 03:33

score 172 · Answer 5 · 2023-10-03T19:18:31.933000

172

Views

Extract summary statistic (beta, SE, EA, non-EA, EA frequency) from csv files (extracted from vcf) not working

Published on 03 October 2023 at 19:18

score 143 · Answer 6 · 2023-05-29T22:56:53.307000

143

Views

Merging two plink files

Published on 29 May 2023 at 22:56

score 507 · Answer 7 · 2023-01-28T12:29:08.520000

507

Views

Is It Possible to Calculate Allele Frequency in a VCF File with Python?

Published on 28 January 2023 at 12:29

score 122 · Answer 8 · 2022-11-19T08:42:00.723000

122

Views

python error: Traceback (most recent call last), IndexError: list index out of range

Published on 19 November 2022 at 08:42

score 64 · Answer 9 · 2022-08-18T13:46:52.537000

64

Views

How to configure vcftools in Ubuntu during installation?

Published on 18 August 2022 at 13:46

score 419 · Answer 10 · 2022-05-01T21:20:28.853000

419

Views

Missing data per site

Published on 01 May 2022 at 21:20

score 912 · Answer 11 · 2022-02-13T21:30:45.613000

912

Views

Extract variant positions from VCF dependent on contents of other columns

Published on 13 February 2022 at 21:30

score 2.1k · Answer 12 · 2022-01-21T12:11:35.923000

2.1k

Views

How to run ensembl-vep in conda

Published on 21 January 2022 at 12:11

score 1.2k · Answer 13 · 2021-12-17T17:14:05.290000

1.2k

Views

VCF file is missing mandatory header line ("#CHROM...")

Published on 17 December 2021 at 17:14

score 583 · Answer 14 · 2021-11-16T14:10:08.747000

583

Views

creating a per sample table from a vcf using bcftools

Published on 16 November 2021 at 14:10

score 304 · Answer 15 · 2021-10-27T03:36:49.893000

304

Views

Problems getting two output files in Nextflow

Published on 27 October 2021 at 03:36

score 126 · Answer 16 · 2021-10-17T07:29:55.737000

126

Views

Merge three columns in one (linux, python, or perl)

Published on 17 October 2021 at 07:29

score 162 · Answer 17 · 2021-07-12T09:34:40.350000

162

Views

match 1,2,5 columns of file1 with 1,2,3 columns of file2 respectively and output should have matched rows from file 2. second file is zipped file .gz

Published on 12 July 2021 at 09:34

score 128 · Answer 18 · 2021-03-11T16:13:19.233000

128

Views

Genetic differentiation in R, function genetic_diff()

Published on 11 March 2021 at 16:13

score 669 · Answer 19 · 2021-02-06T23:36:26.483000

669

Views

How to extract genotype information for each sample as a string from a VCF file using htslib?

Published on 06 February 2021 at 23:36

score 905 · Answer 20 · 2021-01-25T08:31:33.207000

905

Views

How can I filter by read depth using vcftools?

Published on 25 January 2021 at 08:31

List Question

I merged 2 VCF files using bcftools, however how should I update the fields according to 2 VCF files

Filtering VCF files with bcftools

Separating alleles for 'bcftools merge' when ploidy >2

How to extract all variant alleles that do not match "./." from the GT column of a vcf file?

Extract summary statistic (beta, SE, EA, non-EA, EA frequency) from csv files (extracted from vcf) not working

Merging two plink files

Is It Possible to Calculate Allele Frequency in a VCF File with Python?

python error: Traceback (most recent call last), IndexError: list index out of range

How to configure vcftools in Ubuntu during installation?

Missing data per site

Extract variant positions from VCF dependent on contents of other columns

How to run ensembl-vep in conda

VCF file is missing mandatory header line ("#CHROM...")

creating a per sample table from a vcf using bcftools

Problems getting two output files in Nextflow

Merge three columns in one (linux, python, or perl)

match 1,2,5 columns of file1 with 1,2,3 columns of file2 respectively and output should have matched rows from file 2. second file is zipped file .gz

Genetic differentiation in R, function genetic_diff()

How to extract genotype information for each sample as a string from a VCF file using htslib?

How can I filter by read depth using vcftools?

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