phenotype command

[BingLi17]

After changing vtools import CEU.vcf.gz --build hg18 --var_info DP --geno_info DP_geno to vtools import CEU.vcf.gz --build hg38 --var_info DP --geno_info DP_geno

vtools phenotype --output sample_name sample_wildtype BMI 
ERROR: no such column: sample_wildtype

Also some outputs in this page are different from in the vtools documentation.

[BingLi17]

Also liftover:

$ vtools liftover hg19
No data is available.
$ vtools liftover hg38
WARNING: Disable alternative reference genome because of missing column alt_bin, alt_chr, alt_pos.
No data is available.

[BingLi17]

Also show:

$  vtools show annotations | head -50

CancerGeneCensus-20111215 Cancer Genome Project
CancerGeneCensus-20120315 Cancer Genome Project
CancerGeneCensus-20130711 This database contains variants from the Cancer
                        Genome Project. It is an ongoing effort to catalogue
                        those genes for which mutations have been causally
                        implicated in cancer. The original census and
                        analysis was published in Nature Reviews Cancer and
                        supplemental analysis information related to the
                        paper is also available. Currently, more than 1% of
                        all human genes are implicated via mutation in
                        cancer. Of these, approximately 90% have somatic
                        mutations in cancer, 20% bear germline mutations
                        that predispose to cancer and 10% show both somatic
                        and germline mutations.
CancerGeneCensus-20170912 This database contains variants from the Cancer
                        Genome Project. It is an ongoing effort to catalogue
                        those genes for which mutations have been causally
                        implicated in cancer. The original census and
                        analysis was published in Nature Reviews Cancer and
                        supplemental analysis information related to the
                        paper is also available. Currently, more than 1% of
                        all human genes are implicated via mutation in
                        cancer. Of these, approximately 90% have somatic
                        mutations in cancer, 20% bear germline mutations
                        that predispose to cancer and 10% show both somatic
                        and germline mutations.
CosmicCodingMuts-v61_260912 Cosmic coding mutation database.  This data
                        contains mutations affecting 10 or less nucleotides
                        in REF.  The mutation data was obtained from the
                        Sanger Institute Catalogue Of Somatic Mutations In
                        Cancer web site, http://www.sanger.ac.uk/cosmic.
                        Bamford et al (2004). The COSMIC (Catalogue of
                        Somatic Mutations in Cancer) database and website.
                        Br J Cancer, 91,355-358.
CosmicCodingMuts-v67_20131024 Cosmic coding mutation database.  This data
                        contains mutations affecting 10 or less nucleotides
                        in REF.  The mutation data was obtained from the
                        Sanger Institute Catalogue Of Somatic Mutations In
                        Cancer web site, http://www.sanger.ac.uk/cosmic.
                        Bamford et al (2004). The COSMIC (Catalogue of
                        Somatic Mutations in Cancer) database and website.
                        Br J Cancer, 91,355-358.
CosmicCodingMuts-v82_20170801 Cosmic coding mutation database.  This data
                        contains mutations affecting 10 or less nucleotides
                        in REF.  The mutation data was obtained from the
                        Sanger Institute Catalogue Of Somatic Mutations In
                        Cancer web site, http://cancer.sanger.ac.uk/cosmic.
                        The COSMIC (Catalogue of Somatic Mutations in
                        Cancer) database and website. Br J Cancer,
                        91,355-358.
ERROR: [Errno 32] Broken pipe
Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>
BrokenPipeError: [Errno 32] Broken pipe

[BingLi17]

Show:

vtools show annotation knownGene
ERROR: Database knownGene is not currently used in the project.

[BoPeng]

For the last one, vtools use knownGene is needed before the show command.

[BoPeng]

$ vtools show annotations | head -50

The broken pipe thing is because of the use of pipe from command line. The problem was ignored in python2 and but shows in python 3.

[BoPeng]

lifeover needs to have data. Check if the project is currently empty.

[BoPeng]

vtools phenotype first check if phenotype is imported properly (e.g. vtools show phenotype.

[BingLi17]

update

$ vtools update variant --from_stat 'num=#(GT)'
Counting variants:   0.0% [>                                                     ]  in 00:00:00ERROR: near "select": syntax error

[BingLi17]

use

$vtools use dbSNP
 INFO: Choosing version dbSNP-hg18_130 from 10 available databases.
INFO: Downloading annotation database annoDB/dbSNP-hg18_130.ann
INFO: Downloading annotation database from annoDB/dbSNP-hg18_130.DB.gz
dbSNP-hg18_130.DB.gz: 100% [=================================] 617,049,496.0 1.3M/s in 00:07:38

why choose hg18_130?

[BoPeng]

vtools use will choose the latest version of annotation database that matches the primary reference genome of your project. Use vtools show to check the reference genome of the project.

[jma7]

Should we set a default reference genome? @BoPeng

[BoPeng]

No because it is determined by your data. The primary reference genome is set either

vtools init --build

or

vtools import data --build

so users would be in trouble if a default reference genome does not match the one used by the data.

I believe the latest version (hg38) would be used if you do not specify --build anywhere and try to run vtools use someAnnoDB.

[jma7]

Please indicate the commands are from which markdown file, maybe add the line number from the markdown too. @tutudong

[jma7]

These issues have been addressed.