Restrict to highest priority (i.e, priority==1) candidates
$ gemini comp_hets \
--columns "chrom, start, end, gene, impact, cadd_raw" \
trio.trim.vep.recessive.db \
| awk '$14==1' \
| head
chrom
start
end
gene
impact
cadd_raw
variant_id
family_id
family_members
family_genotypes
samples
family_count
comp_het_id
priority
chr15
89398552
89398553
ACAN
non_syn_coding
2.57
9519
family1
1805;unaffected,1847;unaffected,4805;affected
C/A,C/C,A|C
4805
1
52_9519_9534
1
chr15
89417237
89417238
ACAN
non_syn_coding
-‐0.06
9534
family1
1805;unaffected,1847;unaffected,4805;affected
A/A,A/G,A|G
4805
1
52_9519_9534
1
chr15
89398552
89398553
ACAN
non_syn_coding
2.57
9519
family1
1805;unaffected,1847;unaffected,4805;affected
C/A,C/C,A|C
4805
1
53_9519_9535
1
chr15
89417628
89417629
ACAN
splice_region
-‐0.18
9535
family1
1805;unaffected,1847;unaffected,4805;affected
G/G,G/A,G|A
4805
1
53_9519_9535
1
chr2
111598957
111598958
ACOXL
non_syn_coding
0.95
3247
family1
1805;unaffected,1847;unaffected,4805;affected
C/C,C/T,C|T
4805
1
86_3247_3251
1
chr2
111850514
111850515
ACOXL
non_syn_coding
3.17
3251
family1
1805;unaffected,1847;unaffected,4805;affected
C/T,C/C,T|C
4805
1
86_3247_3251
1
chr17
55182877
55182878
AKAP1
non_syn_coding
2.57
13305
family1
1805;unaffected,1847;unaffected,4805;affected
C/T,C/C,T|C
4805
1
104_13305_13308
1
chr17
55183316
55183317
AKAP1
synonymous_coding
0.43
13308
family1
1805;unaffected,1847;unaffected,4805;affected
G/G,G/A,G|A
4805
1
104_13305_13308
1
chr2
29448409
29448410
ALK
non_syn_coding
1.49
839
family1
1805;unaffected,1847;unaffected,4805;affected
T/T,T/G,T|G
4805
1
186_839_841
1
chr2
29455198
29455199
ALK
non_syn_coding
3.51
841
family1
1805;unaffected,1847;unaffected,4805;affected
A/T,A/A,T|A
4805
1
186_839_841
1
$ gemini comp_hets \
--columns "chrom, start, end, gene, impact, cadd_raw" \
trio.trim.vep.recessive.db \
| awk '$14==1' \
| wc -l
612
lines
Each compund heterozygote is a set of two lines, so we have 306 (612 /
2) compound heterozygote candidates
Note: copy and paste the full command from the Github Gist
16