GTGEN¶
The GTGEN command is used to generate genotypes in a horizontal bucket format, e.g. with one or more rows per variant
(chrom,pos,ref,alt) and bucket and values column to store the genotypes as characters (0,1,2,3). The input is a
input stream of row-based variants with a genotype column (GT), a tagbucketrelation and coverage relation.
The GT column (0,1,2,3) is mapped to a bucket and the horizontal character seat in the Values.
GT in rows with empty tag value (PN) are not put into the value column, but can be used to enforce that
a variant row is present for each bucket (see the -u option in CSVCC and CSVSEL).
A presence of a coverage segment (per tag PN) indicates sufficient coverage, i.e. missing variant data (GT not 0,1, or 3)
is interpreted as homozygous reference.
Usage¶
gor ... | GTGEN tagbucketrelation coveragefile [ attributes ]
Options¶
|
Grouping columns other than (chrom,pos) |
|
Override the default PN colunm name used to represent the tag value. |
|
The maximum span size of the coverage segments. Defaults to 10000 (10kb). |
Examples¶
/* An example of creating horizontal variations stored in buckets */
create #PNbuckets# = nor -asdict #wesVars# | SELECT #2 | RENAME #1 PN | ROWNUM
| CALC bucket 'bucket'+str(div((rownum-1),500)+1) | SELECT PN,bucket | SORT -c PN;
create #allvars# = gor #wesvars# -ff [#PNbuckets#] -s PN | SELECT 1-8,PN | DISTINCT;
create #horvars# = gor [#allvars#]
| CALC GT IF( Depth = 9999 OR GL_Call >= 5 AND Depth >= 8 AND
(CallCopies = 2 AND CallRatio >= 0.66 OR CallCopies = 1 AND CallRatio >= 0.2
AND CallRatio <= 1.0-0.2), CallCopies, 3)
| gtgen -gc #3,#4 [#PNbuckets#] <(gor source/cov/goodcov_8.wgs.gord -s PN -ff [#PNbuckets#]);
/* Selecting a random subset of PNs*/
gor [#horvars#] | CSVSEL [#PNbuckets#] <(nor [#PNbuckets#] | SELECT PN | WHERE random() < 0.05) -gc #3,#4 -u 3
The above query example generates a tag-bucket relation and a GOR relation with all variants.
The GTGEN command generates horizontal genotypes from the sparse row-based genotypes, based on
the PN-bucket structure, the quality of the variants and the presence of coverage information. The
output has a bucket column and values column storing the genotypes of the PN as a single character (0,1,2, or 3)
according to the position within the bucket.
For comparison, the #horvar# query can also be generated in the following manner using left-join logic, although it is much less efficient.
create #horvars# = gor [#allvars#] | SELECT 1-4 | MULTIMAP -cartesian -h [#PNbuckets#]
| VARJOIN -r -l -e 0 -xl pn -xr pn <(gor #wesVars# -ff [#PNbuckets#]
| CALC qual IF( Depth = 9999 OR GL_Call >= 5 AND Depth >= 8 AND
(CallCopies = 2 AND CallRatio >= 0.66 OR CallCopies = 1 AND CallRatio >= 0.2
AND CallRatio <= 1.0-0.2),1,-1)
| SELECT 1-4,PN,callcopies,qual )
| JOIN -snpseg -l -r -maxseg 10000 -e 0 -xl pn -xr pn
<(gor source/cov/goodcov_8.wgs.gord -s PN -ff [#PNbuckets#] | CALC goodcov 1)
| REPLACE callcopies IF(qual=-1,'NA',IF(callcopies='0' AND goodcov=0,'NA',callcopies))
| SORT 1 -c #3,#4,PN | GROUP 1 -gc #3-#4,bucket -sc callcopies -lis -len 100000
| RENAME lis_CallCopies values | SELECT 1-4,values,bucket;
Then horizontal variants are then created by expanding each variants with PN and bucket and followed with a left-join into
the sparse variant table #wesVars# and the coverage table. The variant stream is then sorted into a PN order, consistent with the tag-bucket relation, and then collapsed into a comma-separated list per variant. The final query reads a random subset of PNs from the #horvars# relation.
/* Selecting 10 PNs from the first bucket and return as rows */
gor [#horvars#] | CSVSEL -tag PN [#PNbuckets#]
<(nor [#PNbuckets#] | WHERE bucket = 'bucket1' | SELECT #PN | top 10) -gc #3,#4 -u 4
/* Selecting 10 PNs from the first bucket, a slightly faster version */
gor [#horvars#] | WHERE bucket = 'bucket1' | CSVSEL -tag PN [#PNbuckets#]
<(nor [#PNbuckets#] | WHERE bucket = 'bucket1' | SELECT #PN | top 10) -gc #3,#4 -u 4
The last example show how data is read from a table with horizontal buckets and filtered, partially in the reading of the bucket partitions and also in the CSVSEL step.
gor source/hvar/transwgs.gord -nf -ff myPNs.tsv | CSVSEL source/hvar/PNbuckets.tsv myPNs.tsv -gc #3,#4 -u 4