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Change sort order for trio-dnm3 test file #2571

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70 changes: 35 additions & 35 deletions test/trio-dnm3.1.out
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Original file line number Diff line number Diff line change
@@ -1,49 +1,49 @@
dnm21.vcf chr16:28606650 - -inf . . 61 0 100 11,7 0,0 18,0 T,C 0 . . . . .
dnm23.vcf chr9:41644187 - -inf . . 88 0 100 29,4 0,0 20,0 T,A 0 . . . . .
dnm38.vcf chrX:49689611 - -inf . . 33 0 50 4,8 0,0 1,1 T,C 0 . . . . .
dnm17.vcf chrX:141906066 - -544.123 . . 66 0 26 29,57 77,0 168,59 C,G 1 . . . . .
dnm01.vcf chr8:120811802 o -0.764704 . . 18 0 0 9,2,0 71,0,1 56,0,1 G,T,A 1 . . . . .
dnm06.vcf chr6:32522150 - -1.7168 . . 100 0 0 0,26,0,0 1,0,9,0 23,0,0,1 T,G,A,C 1 . . . . .
dnm07.vcf chr9:19094217 --unk -7.01979 . . 62 0 0 4,8,1 3,0,0 13,0,0 G,A,T 1 . . . . .
dnm09.vcf chr2:219571274 - -17.5276 . . 50 0 0 3,5,1,1 9,0,8,2 11,0,4,4 A,G,T,C 1 . . . . .
dnm10.vcf chr8:30846433 o -0.000201919 . . 41 0 0 41,29,1 69,0,0 52,0,0 C,G,T 1 . . . . .
dnm11.vcf chr10:104250407 - -74.5666 . . 66 3 11 19,37 28,1 78,10 G,C 1 . . . . .
dnm12.vcf chr6:32581812 - -330.706 . . 31 8 16 110,50 206,19 140,27 A,C 1 . . . . .
dnm13.vcf chrX:68112092 - -17.7637 . . 100 0 0 8,0 0,5 0,1 G,C 0 . . . . .
dnm14.vcf chr12:27401766 - -11.8629 . . 100 0 0 0,14 4,0 5,0 G,A 1 . . . . .
dnm15.vcf chr6:32581810 - -124.562 . . 18 11 0 178,40 174,22 36,0 T,G 1 . . . . .
dnm16.vcf chr6:32761865 - -88.0806 . . 19 11 0 101,0,24 59,66,16 91,0,0 G,C,A 2 . . . . .
dnm11.vcf chr10:104250407 - -74.5666 . . 66 3 11 19,37 28,1 78,10 G,C 1 . . . . .
dnm13.vcf chrX:68112092 - -17.7637 . . 100 0 0 8,0 0,5 0,1 G,C 0 . . . . .
dnm09.vcf chr2:219571274 - -17.5276 . . 50 0 0 3,5,1,1 9,0,8,2 11,0,4,4 A,G,T,C 1 . . . . .
dnm17.vcf chrX:141906066 - -544.123 . . 66 0 26 29,57 77,0 168,59 C,G 1 . . . . .
dnm18.vcf chr11:71527372 - -15.1104 . . 24 4 0 116,37,1 149,7,0 101,0,1 T,C,G 1 . . . . .
dnm22.vcf chr11:71527372 - -15.1104 . . 24 4 0 116,37,1 149,7,0 101,0,1 T,C,G 1 . . . . .
dnm32.vcf chrM:9899 - -13.155 . . 37 0 2 198,117,1,0 319,0,0,1 313,8,0,0 T,C,A,G 1 . . . . .
dnm14.vcf chr12:27401766 - -11.8629 . . 100 0 0 0,14 4,0 5,0 G,A 1 . . . . .
dnm41.vcf chr1:930055 - -9.54764 . . 100 0 0 0,6 4,0 1,0 C,G 1 . . . . .
dnm19.vcf chr2:165310656 --unk -8.82426 . . 100 0 0 0,9 2,0 7,0 T,A 1 . . . . .
dnm36.vcf chr16:58041597 o-ma -7.22407 . . 49 0 0 30,33,4 58,0,0 43,0,0 G,A,T 1 . . . . .
dnm07.vcf chr9:19094217 --unk -7.01979 . . 62 0 0 4,8,1 3,0,0 13,0,0 G,A,T 1 . . . . .
dnm20.vcf chr7:98949906 --unk -6.33187 . . 70 0 0 8,19 4,0 17,0 C,T 1 . . . . .
dnm30.vcf chr19:13978125 o-mosaic -3.16171 . . 13 0 0 14,2 24,0 26,0 G,A 1 . . . . .
dnm27.vcf chr17:81536135 o-mosaic -2.37269 . . 10 0 0 26,3 45,0 39,0 G,A 1 . . . . .
dnm21.vcf chr16:28606650 - -inf . . 61 0 100 11,7 0,0 18,0 T,C 0 . . . . .
dnm22.vcf chr11:71527372 - -15.1104 . . 24 4 0 116,37,1 149,7,0 101,0,1 T,C,G 1 . . . . .
dnm23.vcf chr9:41644187 - -inf . . 88 0 100 29,4 0,0 20,0 T,A 0 . . . . .
dnm24.vcf chr19:54775322 - -1.90049 . . 13 0 0 109,17 95,0 86,0 G,C 1 . . . . .
dnm06.vcf chr6:32522150 - -1.7168 . . 100 0 0 0,26,0,0 1,0,9,0 23,0,0,1 T,G,A,C 1 . . . . .
dnm28.vcf chr16:2210587 o-mosaic -1.70308 . . 13 0 0 28,4 62,0 43,0 G,C 1 . . . . .
dnm45.vcf chr17:38802154 o-mosaic -1.3055 . . 16 0 0 48,9,0 71,0,0 65,0,1 G,A,T 1 . . . . .
dnm25.vcf chr3:48419708 o-mosaic -1.17026 . . 16 0 0 56,11,1 80,0,0 70,0,0 C,G,T 1 . . . . .
dnm42.vcf chr1:151306305 o-mosaic -1.07353 . . 17 0 0 59,12,1 66,0,0 58,0,0 A,C,T 1 . . . . .
dnm01.vcf chr8:120811802 o -0.764704 . . 18 0 0 9,2,0 71,0,1 56,0,1 G,T,A 1 . . . . .
dnm26.vcf chr19:43071662 o -5.06194e-07 . . 51 0 0 38,39 117,0 101,0 C,A 1 . . . . .
dnm27.vcf chr17:81536135 o-mosaic -2.37269 . . 10 0 0 26,3 45,0 39,0 G,A 1 . . . . .
dnm28.vcf chr16:2210587 o-mosaic -1.70308 . . 13 0 0 28,4 62,0 43,0 G,C 1 . . . . .
dnm29.vcf chr1:39901935 --unk -0.457031 . . 23 0 0 10,3 22,0 26,0 G,C 1 . . . . .
dnm40.vcf chr1:35192655 o -0.336011 . . 23 0 0 62,18 92,0 67,0 G,A 1 . . . . .
dnm51.vcf chr11:62604250 o-pdp -0.253838 . . 46 0 0 13,11 15,0 23,0 G,A 1 . . . . .
dnm50.vcf chr1:39452137 o-mosaic -0.209761 . . 26 0 0 17,6 31,0 25,0 C,T 1 . . . . .
dnm53.vcf chr18:31466562 --unk -0.206326 . . 29 0 0 37,15 57,0 48,0 T,G 1 . . 65 0 0
dnm30.vcf chr19:13978125 o-mosaic -3.16171 . . 13 0 0 14,2 24,0 26,0 G,A 1 . . . . .
dnm31.vcf chr7:114922376 o -0.124865 . . 50 0 5 17,17 30,0 20,1 G,A 1 . . . . .
dnm32.vcf chrM:9899 - -13.155 . . 37 0 2 198,117,1,0 319,0,0,1 313,8,0,0 T,C,A,G 1 . . . . .
dnm33.vcf chr6:32518660 - -0.176899 . . 27 0 5 40,15 23,0 42,2 T,C 1 . . . . .
dnm34.vcf chr16:90035660 o -2.39592e-05 . . 45 3 0 44,36 67,2 82,0 C,T 1 . . . . .
dnm35.vcf chr2:95951365 - -0.00159963 . . 38 4 0 60,36 45,2 64,0 G,A 1 . . . . .
dnm36.vcf chr16:58041597 o-ma -7.22407 . . 49 0 0 30,33,4 58,0,0 43,0,0 G,A,T 1 . . . . .
dnm37.vcf chr19:54751586 - -0.172621 . . 57 0 3 3,4 16,0 28,1 G,A 1 . . . . .
dnm43.vcf chr7:74097029 o -0.144411 . . 48 0 0 15,14 16,0 48,0 G,A 1 . . . . .
dnm52.vcf chr11:64320638 o-pdp -0.144198 . . 56 0 0 12,15 16,0 34,0 G,A 1 . . . . .
dnm31.vcf chr7:114922376 o -0.124865 . . 50 0 5 17,17 30,0 20,1 G,A 1 . . . . .
dnm38.vcf chrX:49689611 - -inf . . 33 0 50 4,8 0,0 1,1 T,C 0 . . . . .
dnm39.vcf chr6:31356309 - -0.121649 . . 100 4 3 0,5 24,1 37,1 G,C 1 . . . . .
dnm49.vcf chr21:39312993 - -0.10072 . . 29 0 0 22,9 21,0 23,0 G,C 1 . . . . .
dnm54.vcf chr2:232380380 o -0.00690831 . . 51 0 0 34,35,0 41,0,36 74,0,0 A,C,G 1 . . 3 4 0
dnm48.vcf chr3:195783381 - -0.00176814 . . 54 0 0 19,22 16,0 27,0 G,C 1 . . . . .
dnm35.vcf chr2:95951365 - -0.00159963 . . 38 4 0 60,36 45,2 64,0 G,A 1 . . . . .
dnm10.vcf chr8:30846433 o -0.000201919 . . 41 0 0 41,29,1 69,0,0 52,0,0 C,G,T 1 . . . . .
dnm46.vcf chr9:137114271 o -3.01723e-05 . . 45 0 2 27,22 54,0 65,1 C,T 1 . . . . .
dnm34.vcf chr16:90035660 o -2.39592e-05 . . 45 3 0 44,36 67,2 82,0 C,T 1 . . . . .
dnm40.vcf chr1:35192655 o -0.336011 . . 23 0 0 62,18 92,0 67,0 G,A 1 . . . . .
dnm41.vcf chr1:930055 - -9.54764 . . 100 0 0 0,6 4,0 1,0 C,G 1 . . . . .
dnm42.vcf chr1:151306305 o-mosaic -1.07353 . . 17 0 0 59,12,1 66,0,0 58,0,0 A,C,T 1 . . . . .
dnm43.vcf chr7:74097029 o -0.144411 . . 48 0 0 15,14 16,0 48,0 G,A 1 . . . . .
dnm44.vcf chr18:76910115 o -8.46558e-07 . . 50 0 1 46,46,0 39,0,0 88,1,1 T,A,G 1 . . . . .
dnm26.vcf chr19:43071662 o -5.06194e-07 . . 51 0 0 38,39 117,0 101,0 C,A 1 . . . . .
dnm45.vcf chr17:38802154 o-mosaic -1.3055 . . 16 0 0 48,9,0 71,0,0 65,0,1 G,A,T 1 . . . . .
dnm46.vcf chr9:137114271 o -3.01723e-05 . . 45 0 2 27,22 54,0 65,1 C,T 1 . . . . .
dnm47.vcf chrX:136240391 o -2.09988e-08 . . 100 0 0 0,37 26,0 61,0 C,T 1 . . . . .
dnm48.vcf chr3:195783381 - -0.00176814 . . 54 0 0 19,22 16,0 27,0 G,C 1 . . . . .
dnm49.vcf chr21:39312993 - -0.10072 . . 29 0 0 22,9 21,0 23,0 G,C 1 . . . . .
dnm50.vcf chr1:39452137 o-mosaic -0.209761 . . 26 0 0 17,6 31,0 25,0 C,T 1 . . . . .
dnm51.vcf chr11:62604250 o-pdp -0.253838 . . 46 0 0 13,11 15,0 23,0 G,A 1 . . . . .
dnm52.vcf chr11:64320638 o-pdp -0.144198 . . 56 0 0 12,15 16,0 34,0 G,A 1 . . . . .
dnm53.vcf chr18:31466562 --unk -0.206326 . . 29 0 0 37,15 57,0 48,0 T,G 1 . . 65 0 0
dnm54.vcf chr2:232380380 o -0.00690831 . . 51 0 0 34,35,0 41,0,36 74,0,0 A,C,G 1 . . 3 4 0
3 changes: 2 additions & 1 deletion test/trio-dnm3/test.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,9 @@
cd "$(dirname "${BASH_SOURCE[0]}")"

BCFTOOLS=${1:-bcftools}
export LC_ALL=C

for x in *.vcf; do
"$BCFTOOLS" +trio-dnm3 -p 1X:child,dad,mom $x | "$BCFTOOLS" query -uf$x'\t%CHROM:%POS\t%EXP\t[ %DNM]\t[ %VAF]\t[ %AD]\t%REF,%ALT\t[ %VA]\t[ %SP]';
done | sort -k3,3g -k4,4g -k3,3d | sed 's,fp,-, ; s,tp,o,'
done | sort | sed 's,fp,-, ; s,tp,o,'

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