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BENCHMARKS_chr20
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Chr20 of NA12878 ~33x
---------------------
15736158 reads, 2284356072 bp, avg 145.166 length.
chr20_lossy.6: current snp_score as of 8th Jan 2016
#define QL 10
#define QM 25 // below => QL, else QH
#define QH 40
#define M 0
// Whether to reduce quality on mismatching bases (ie QL)
#define REDUCE_QUAL 1
#define STR_DIST 2
// Standard gap5 algorithm; set MIN_QUAL_A to 0 to disable
#define MIN_QUAL_A 30
#define MIN_INDEL_A 50
#define MIN_DISCREP_A 2.0
// With mqual adjustment; set MIN_QUAL_B to 0 to disable
#define MIN_QUAL_B 75
#define MIN_INDEL_B 150
#define MIN_DISCREP_B 1.0
@ seq3a[scratch01/jkb]; cram_size 13502_7_chr20_lossy.6.cram | grep QS
Block content_id 12, total size 37050254 R QS
@ seq3a[scratch01/jkb]; cram_size 13502_7_chr20_orig.cram | grep QS
Block content_id 12, total size 482056158 R QS
Orig vs new:
Freebayes SNPs 99.97% precision 99.94% recall
Freebayes Indel 99.99% precision 99.89% recall
Orig vs Platinum Genomes:
Freebayes SNPs 93.01% precision 91.11% recall
Freebayes Indel 77.34% precision 72.77% recall
Lossy vs Platinum Genomes:
Freebayes SNPs 93.03% precision 91.11% recall
Freebayes Indel 77.34% precision 72.77% recall
Absolute terms, from orig -> lossy
SNPS: -19 false positive, -1 false negative
Indel: -7 false positive, +7 false negative
ID 0 13502_7_chr20_orig.bam.freebayes.norm.vcf.gz
ID 1 13502_7_chr20_lossy.6.cram.freebayes.norm.vcf.gz
ID 2 13502_7_chr20_orig.bam.freebayes.norm.vcf.gz 13502_7_chr20_lossy.6.cram.freebayes.norm.vcf.gz
# SN, Summary numbers:
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 1 number of samples: 1
SN 0 number of records: 58
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 37
SN 0 number of MNPs: 8
SN 0 number of indels: 16
SN 0 number of others: 0
SN 0 number of multiallelic sites: 6
SN 0 number of multiallelic SNP sites: 1
SN 1 number of records: 26
SN 1 number of no-ALTs: 0
SN 1 number of SNPs: 22
SN 1 number of MNPs: 5
SN 1 number of indels: 2
SN 1 number of others: 0
SN 1 number of multiallelic sites: 3
SN 1 number of multiallelic SNP sites: 0
SN 2 number of records: 91877
SN 2 number of no-ALTs: 0
SN 2 number of SNPs: 75949
SN 2 number of MNPs: 1813
SN 2 number of indels: 13977
SN 2 number of others: 756
SN 2 number of multiallelic sites: 1265
SN 2 number of multiallelic SNP sites: 12
# QUAL, Stats by quality:
# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels
QUAL 0 0 27 8 19 0
QUAL 0 1 2 1 1 0
QUAL 0 6 1 0 1 0
QUAL 0 10 1 1 0 0
QUAL 0 14 1 0 1 0
QUAL 0 16 1 1 0 0
QUAL 0 83 0 0 0 1
QUAL 0 84 0 0 0 1
QUAL 0 122 0 0 0 1
QUAL 0 133 0 0 0 1
QUAL 0 143 1 0 1 0
QUAL 0 150 0 0 0 1
QUAL 0 157 0 0 0 1
QUAL 0 167 0 0 0 1
QUAL 0 184 0 0 0 1
QUAL 0 286 0 0 0 1
QUAL 0 288 0 0 0 1
QUAL 0 328 0 0 0 1
QUAL 0 339 0 0 0 1
QUAL 0 355 1 0 0 1
QUAL 0 400 1 0 0 1
QUAL 0 409 0 0 0 1
QUAL 0 464 1 0 0 1
QUAL 1 0 10 4 6 0
QUAL 1 2 1 0 1 0
QUAL 1 3 1 0 1 0
QUAL 1 17 1 1 0 0
QUAL 1 25 1 0 1 0
QUAL 1 44 1 1 0 0
QUAL 1 57 1 0 1 0
QUAL 1 179 1 0 0 0
QUAL 1 217 0 0 0 1
QUAL 1 268 1 0 0 0
QUAL 1 314 1 1 0 0
QUAL 1 336 1 1 0 0
QUAL 1 355 1 0 0 0
QUAL 1 368 1 1 0 0
QUAL 1 395 0 0 0 1
bcftools isec to find true calls on the lossless set that are no
longer called by the lossy set... isec plat orig, isec plat lossy,
isec orig/3 lossy/3.
/tmp/_isec/0000.vcf for records private to /tmp/_lossy/0003.vcf.gz
/tmp/_isec/0001.vcf for records private to /tmp/_orig/0003.vcf.gz
Lost correct calls:
@ seq3a[scratch01/jkb]; egrep -v '^#' /tmp/_isec/0001.vcf|cut -c 1-60
20 2052937 . T TA 84.3078 . AB=0.291667;ABP=12.0581;AC=1;AF=
20 4987594 . C CGT 167.933 . AB=0.25;ABP=20.3821;AC=1;AF=0.5
20 11323168 . T TTGTGTGTG 83.2128 . AB=0.26087;ABP=14.4341;A
20 16720550 . A AT 133.113 . AB=0.24;ABP=17.6895;AC=1;AF=0.5
20 37814029 . G GCACACA 157.624 . AB=0.259259;ABP=16.6021;AC
20 40675418 . A AGTGTGTGTGTGT 150.974 . AB=0.21875;ABP=24.99
20 42904995 . A AAAGGAAGGAAGG,AAAGGAAGGAAGGAAGG 328.509 . AB
20 47226827 . C CTCTT 184.517 . AB=0.269231;ABP=15.0369;AC=1
20 55765469 . C A 143.949 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;C
20 57002291 . A G 10.7264 . AB=0.227273;ABP=17.2236;AC=1;AF=
Gained correct calls:
@ seq3a[scratch01/jkb]; egrep -v '^#' /tmp/_isec/0000.vcf|cut -c 1-60
20 29436239 . T C 314.787 . AB=0.258065;ABP=34.5317;AC=1;AF=
20 29648764 . T C 44.3879 . AB=0.205882;ABP=28.557;AC=1;AF=0
20 50275429 . G GTGGGGC 395.448 . AB=0.375;ABP=6.26751;AC=1;
20 50336285 . G A 368.492 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=12;
..................................................
Samtools:
Orig vs Platinum Genomes:
Samtools SNPs 95.22% precision 94.85% recall
Samtools Indel 78.50% precision 61.78% recall
Lossy vs Platinum Genomes:
Samtools SNPs 95.20% precision 94.85% recall
Samtools Indel 78.34% precision 62.09% recall
Absolute terms, from orig -> lossy
SNPS: +28 false positive, -3 false negative
Indel: +36 false positive, -46 false negative
ID 0 13502_7_chr20_orig.bam.samtools.norm.vcf.gz
ID 1 13502_7_chr20_lossy.6.cram.samtools.norm.vcf.gz
ID 2 13502_7_chr20_orig.bam.samtools.norm.vcf.gz 13502_7_chr20_lossy.6.cram.samtools.norm.vcf.gz
# SN, Summary numbers:
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 1 number of samples: 1
SN 0 number of records: 59
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 10
SN 0 number of MNPs: 0
SN 0 number of indels: 49
SN 0 number of others: 0
SN 0 number of multiallelic sites: 6
SN 0 number of multiallelic SNP sites: 0
SN 1 number of records: 172
SN 1 number of no-ALTs: 0
SN 1 number of SNPs: 41
SN 1 number of MNPs: 0
SN 1 number of indels: 131
SN 1 number of others: 0
SN 1 number of multiallelic sites: 7
SN 1 number of multiallelic SNP sites: 0
SN 2 number of records: 90735
SN 2 number of no-ALTs: 0
SN 2 number of SNPs: 79092
SN 2 number of MNPs: 0
SN 2 number of indels: 11643
SN 2 number of others: 0
SN 2 number of multiallelic sites: 786
SN 2 number of multiallelic SNP sites: 17
# QUAL, Stats by quality:
# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels
QUAL 0 3 1 1 0 7
QUAL 0 4 3 1 2 11
QUAL 0 5 0 0 0 9
QUAL 0 6 1 0 1 4
QUAL 0 7 1 1 0 3
QUAL 0 8 1 1 0 1
QUAL 0 11 0 0 0 1
QUAL 0 12 1 1 0 1
QUAL 0 13 1 1 0 0
QUAL 0 14 0 0 0 1
QUAL 0 20 1 0 1 0
QUAL 0 24 0 0 0 1
QUAL 0 32 0 0 0 1
QUAL 0 35 0 0 0 1
QUAL 0 45 0 0 0 1
QUAL 0 52 0 0 0 1
QUAL 0 69 0 0 0 1
QUAL 0 184 0 0 0 1
QUAL 0 192 0 0 0 1
QUAL 0 195 0 0 0 2
QUAL 0 198 0 0 0 1
QUAL 1 3 10 2 8 28
QUAL 1 4 5 1 4 26
QUAL 1 5 7 5 2 15
QUAL 1 6 1 0 1 12
QUAL 1 7 5 3 2 11
QUAL 1 8 2 0 2 5
QUAL 1 9 0 0 0 8
QUAL 1 10 2 1 1 3
QUAL 1 11 2 1 1 1
QUAL 1 12 2 0 2 2
QUAL 1 13 1 0 1 1
QUAL 1 14 0 0 0 1
QUAL 1 15 0 0 0 1
QUAL 1 16 0 0 0 2
QUAL 1 17 2 1 1 1
QUAL 1 18 0 0 0 1
Plat20 vs Orig
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 /nfs/users/nfs_j/jkb/work/qual_loss/plat20n-.vcf.gz
ID 1 13502_7_chr20_orig.bam.samtools.norm.vcf.gz
ID 2 /nfs/users/nfs_j/jkb/work/qual_loss/plat20n-.vcf.gz 13502_7_chr20_orig.bam.samtools.norm.vcf.gz
# SN, Summary numbers:
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 1 number of samples: 1
SN 0 number of records: 9731
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 4094
SN 0 number of MNPs: 0
SN 0 number of indels: 5679
SN 0 number of others: 15
SN 0 number of multiallelic sites: 656
SN 0 number of multiallelic SNP sites: 16
SN 1 number of records: 6288
SN 1 number of no-ALTs: 0
SN 1 number of SNPs: 3774
SN 1 number of MNPs: 0
SN 1 number of indels: 2514
SN 1 number of others: 0
SN 1 number of multiallelic sites: 490
SN 1 number of multiallelic SNP sites: 3
SN 2 number of records: 84506
SN 2 number of no-ALTs: 0
SN 2 number of SNPs: 75328
SN 2 number of MNPs: 0
SN 2 number of indels: 9178
SN 2 number of others: 0
SN 2 number of multiallelic sites: 302
SN 2 number of multiallelic SNP sites: 14
Plat20 vs Lossy
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 /nfs/users/nfs_j/jkb/work/qual_loss/plat20n-.vcf.gz
ID 1 13502_7_chr20_lossy.6.cram.samtools.norm.vcf.gz
ID 2 /nfs/users/nfs_j/jkb/work/qual_loss/plat20n-.vcf.gz 13502_7_chr20_lossy.6.cram.samtools.norm.vcf.gz
# SN, Summary numbers:
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 1 number of samples: 1
SN 0 number of records: 9682
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 4091
SN 0 number of MNPs: 0
SN 0 number of indels: 5633
SN 0 number of others: 15
SN 0 number of multiallelic sites: 652
SN 0 number of multiallelic SNP sites: 16
SN 1 number of records: 6352
SN 1 number of no-ALTs: 0
SN 1 number of SNPs: 3802
SN 1 number of MNPs: 0
SN 1 number of indels: 2550
SN 1 number of others: 0
SN 1 number of multiallelic sites: 487
SN 1 number of multiallelic SNP sites: 3
SN 2 number of records: 84555
SN 2 number of no-ALTs: 0
SN 2 number of SNPs: 75331
SN 2 number of MNPs: 0
SN 2 number of indels: 9224
SN 2 number of others: 0
SN 2 number of multiallelic sites: 306
SN 2 number of multiallelic SNP sites: 14
Winners and losers (orig vs plat // lossy vs plat):
/tmp/_isec2/0000.vcf for records private to /tmp/_lossy2/0003.vcf.gz
/tmp/_isec2/0001.vcf for records private to /tmp/_orig2/0003.vcf.gz
Lost correct calls:
@ seq3a[scratch01/jkb]; egrep -v '^#' /tmp/_isec2/0001.vcf|cut -c 1-60
20 2760359 . C CA 5.26339 . INDEL;IDV=19;IMF=0.542857;DP=35;
20 7510267 . TAA T 4.58681 . INDEL;IDV=8;IMF=0.32;DP=22;VDB=
20 10914114 . T TA 3.22773 . INDEL;IDV=17;IMF=0.447368;DP=38
20 11807903 . T TA 4.87657 . INDEL;IDV=20;IMF=0.487805;DP=41
20 12245133 . C CA 5.35199 . INDEL;IDV=5;IMF=0.227273;DP=22;
20 18057119 . T G 6.35454 . DP=30;VDB=0.0411132;SGB=-0.51153
20 18190157 . G C 4.42775 . DP=3;VDB=0.827271;SGB=-0.511536;
20 21239702 . C CA 3.29908 . INDEL;IDV=14;IMF=0.4375;DP=32;V
20 29835401 . A AAAC 5.98068 . INDEL;IDV=5;IMF=0.185185;DP=2
20 38349001 . CA C 4.40112 . INDEL;IDV=17;IMF=0.377778;DP=45
20 40392561 . A G 8.05252 . DP=28;VDB=0.14;SGB=-0.453602;MQS
20 41077498 . TA T 6.48339 . INDEL;IDV=19;IMF=0.513514;DP=37
20 41748917 . G GT 7.4721 . INDEL;IDV=12;IMF=0.444444;DP=27;
20 41918730 . C CA 5.80944 . INDEL;IDV=19;IMF=0.558824;DP=34
20 43063165 . G C 4.75718 . DP=200;VDB=0.235908;SGB=-0.68064
20 43549791 . AT A 4.86163 . INDEL;IDV=21;IMF=0.567568;DP=36
20 46433932 . G C 20.7664 . DP=38;VDB=0.0797974;SGB=-0.55641
20 54981173 . GT G 3.75223 . INDEL;IDV=19;IMF=0.339286;DP=56
20 56407989 . G GA 4.12161 . INDEL;IDV=12;IMF=0.3;DP=40;VDB=
20 59822403 . G GC 8.01996 . INDEL;IDV=32;IMF=0.376471;DP=85
(All low conf, highest being 20.7664)
Gained correct calls:
@ seq3a[scratch01/jkb]; egrep -v '^#' /tmp/_isec2/0000.vcf|cut -c 1-60
20 570945 . A AACAC,AAC 194 . INDEL;IDV=25;IMF=0.714286;DP=3
20 2008442 . C CT 3.78439 . INDEL;IDV=13;IMF=0.464286;DP=28;
20 2504625 . CAAA C 8.10251 . INDEL;IDV=5;IMF=0.25;DP=19;VDB
20 2617105 . TAC T,TACACACACACAC 186 . INDEL;IDV=13;IMF=0.52
20 3191722 . AAAG A 7.58795 . INDEL;IDV=4;IMF=0.173913;DP=23
20 3549166 . A AT 3.7418 . INDEL;IDV=10;IMF=0.434783;DP=23;V
20 4232706 . C CT 5.64027 . INDEL;IDV=10;IMF=0.454545;DP=22;
20 4949370 . C CTT 9.93676 . INDEL;IDV=12;IMF=0.342857;DP=35
20 5432204 . A AG 7.31117 . INDEL;IDV=15;IMF=0.394737;DP=36;
20 6897116 . CT C 3.23574 . INDEL;IDV=16;IMF=0.410256;DP=39;
20 7416919 . T TA 3.16796 . INDEL;IDV=12;IMF=0.521739;DP=23;
20 7507268 . A AT 4.36496 . INDEL;IDV=12;IMF=0.631579;DP=19;
20 10467573 . G GT 10.876 . INDEL;IDV=16;IMF=0.516129;DP=31;
20 16451489 . A AT 3.21563 . INDEL;IDV=16;IMF=0.457143;DP=35
20 16937426 . CT C 7.27445 . INDEL;IDV=26;IMF=0.866667;DP=30
20 17295957 . G GA 6.69411 . INDEL;IDV=12;IMF=0.4;DP=30;VDB=
20 19838767 . T TA 7.92229 . INDEL;IDV=14;IMF=0.311111;DP=45
20 19964247 . T TA 3.73813 . INDEL;IDV=14;IMF=0.341463;DP=41
20 20046260 . G GAAA 3.42001 . INDEL;IDV=8;IMF=0.222222;DP=3
20 20144228 . G GT 3.83311 . INDEL;IDV=14;IMF=0.5;DP=28;VDB=
20 20819627 . G GA 4.79399 . INDEL;IDV=12;IMF=0.461538;DP=26
20 21670107 . C CAA 3.92842 . INDEL;IDV=12;IMF=0.428571;DP=2
20 23114997 . C CA 4.53051 . INDEL;IDV=11;IMF=0.6875;DP=16;V
20 23689877 . CTTT C 5.53106 . INDEL;IDV=5;IMF=0.333333;DP=1
20 24985716 . C CA 4.49934 . INDEL;IDV=15;IMF=0.46875;DP=32;
20 25556400 . CA C 5.22439 . INDEL;IDV=26;IMF=0.40625;DP=64;
20 25719486 . TA T 4.7876 . INDEL;IDV=11;IMF=0.34375;DP=32;V
20 30514917 . CA C 5.0712 . INDEL;IDV=15;IMF=0.576923;DP=26;
20 30907330 . T TAC 68 . INDEL;IDV=3;IMF=0.5;DP=6;VDB=0.6404
20 30987905 . T TA 3.182 . INDEL;IDV=14;IMF=0.35;DP=40;VDB=0
20 31209011 . A G 7.16695 . DP=11;SGB=-0.379885;MQ0F=0;AC=2;
20 34006498 . G GA 3.78548 . INDEL;IDV=12;IMF=0.333333;DP=36
20 35237606 . G A 17.1919 . DP=11;VDB=0.663511;SGB=-0.511536
20 35237614 . G A 7.09648 . DP=11;VDB=0.58;SGB=-0.453602;MQS
20 35237622 . G A 34.0876 . DP=11;VDB=0.573211;SGB=-0.556411
20 36150582 . C CA 6.78866 . INDEL;IDV=12;IMF=0.5;DP=24;VDB=
20 36530004 . AC A 5.19411 . INDEL;IDV=14;IMF=0.466667;DP=27
20 37718364 . ATT A 6.55244 . INDEL;IDV=9;IMF=0.346154;DP=26
20 37890448 . A AT 5.90056 . INDEL;IDV=19;IMF=0.5;DP=38;VDB=
20 42051181 . T TA 7.04348 . INDEL;IDV=13;IMF=0.619048;DP=21
20 43659815 . AT A 4.30031 . INDEL;IDV=25;IMF=0.657895;DP=38
20 43931737 . A AAAAG 4.37281 . INDEL;IDV=3;IMF=0.142857;DP=
20 44362554 . AG A 3.87946 . INDEL;IDV=7;IMF=0.411765;DP=17;
20 44370690 . A ATTT 16.2475 . INDEL;IDV=13;IMF=0.282609;DP=
20 44543614 . C CTT 3.48117 . INDEL;IDV=10;IMF=0.285714;DP=3
20 44966226 . G GA 3.7836 . INDEL;IDV=18;IMF=0.352941;DP=51;
20 45623544 . C CT 8.64957 . INDEL;IDV=21;IMF=0.7;DP=30;VDB=
20 46162057 . A ATT 5.26374 . INDEL;IDV=8;IMF=0.363636;DP=22
20 46263664 . CTTT C 9.36947 . INDEL;IDV=7;IMF=0.291667;DP=2
20 46436906 . CAA C 3.7393 . INDEL;IDV=11;IMF=0.366667;DP=28
20 48488994 . CT C 6.07 . INDEL;IDV=26;IMF=0.65;DP=40;VDB=0.
20 49093164 . G GAA 6.50536 . INDEL;IDV=6;IMF=0.24;DP=24;VDB
20 49259829 . T TTG 9.53339 . INDEL;IDV=3;IMF=0.166667;DP=18
20 49364026 . C T 5.84906 . DP=12;VDB=0.1;SGB=-0.453602;RPB=
20 50368592 . CA C 24.7555 . INDEL;IDV=32;IMF=0.627451;DP=51
20 52107618 . AC A 9.8042 . INDEL;IDV=3;IMF=0.157895;DP=18;V
20 52154102 . C CTTT,CTT 43.3914 . INDEL;IDV=14;IMF=0.451613
20 52249677 . CA C 4.83103 . INDEL;IDV=14;IMF=0.583333;DP=23
20 52326240 . TC T 3.21741 . INDEL;IDV=6;IMF=0.222222;DP=27;
20 52524256 . T TAAA 10.3879 . INDEL;IDV=12;IMF=0.375;DP=32;
20 54542633 . GTA G 4.80549 . INDEL;IDV=2;IMF=0.25;DP=8;VDB=
20 54968215 . TACAC TAC,T 194 . INDEL;IDV=21;IMF=0.875;DP=24
20 55588656 . C CAAAAAAAA 85 . INDEL;IDV=9;IMF=0.257143;DP=3
20 57031304 . G T 6.28142 . DP=21;VDB=0.045681;SGB=-0.511536
20 57037899 . C CAAAAAA 8.03588 . INDEL;IDV=4;IMF=0.210526;D
20 60974604 . G GT 5.84439 . INDEL;IDV=12;IMF=0.48;DP=25;VDB
20 61176807 . T C 10.7903 . DP=28;VDB=0.0298006;SGB=-0.55641
20 61421099 . ATT A 4.70259 . INDEL;IDV=10;IMF=0.322581;DP=3
20 62111388 . A G 4.03056 . DP=30;VDB=0.148533;SGB=-0.511536
Several high confidence indels, but all low-ish conf SNPs