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edits
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== Output ==
== Output ==
atks@fantasia:~/data/got2d$ vmatch got2d.wg4x.1511samples.73976indels.gatk.chr20.sites.vcf got2d.wg4x.1514samples.71994indels.samtools.chr20.sites.vcf -w 10 -d
atks@fantasia:~/data/got2d$ vmatch got2d.wg4x.1511samples.73976indels.gatk.chr20.sites.vcf got2d.wg4x.1514samples.71994indels.samtools.chr20.sites.vcf -w 10 -d
VCF file A : got2d.wg4x.1511samples.73976indels.gatk.chr20.sites.vcf
VCF file A : got2d.wg4x.1511samples.73976indels.gatk.chr20.sites.vcf
VCF file B : got2d.wg4x.1514samples.71994indels.samtools.chr20.sites.vcf
VCF file B : got2d.wg4x.1514samples.71994indels.samtools.chr20.sites.vcf
Genome file : /net/fantasia/home/atks/ref/genome/human.g1k.v37.fa
Window Size : 10
Genome file : /net/fantasia/home/atks/ref/genome/human.g1k.v37.fa
SRSA : 8578
Window Size : 10
SRSAN : 34522
SRSA : 8578
SRDA : 2363
SRSAN : 34522
SRDNA : 888
SRDA : 2363
DRDA : 2322
SRDNA : 888
DRDNA : 439
DRDA : 2322
#A Records : 73976
DRDNA : 439
#B Records : 71994
Match %tage for VCF file A
#A Records : 73976
Level 1 (SRSA, SRSAN) : 58.2621
#B Records : 71994
Level 2 (SRSA, SRSAN, SRDA, SRDNA) : 62.6568
Match %tage for VCF file A
Level 3 (SRSA, SRSAN, SRDA, SRDNA, DRDA, DRDNA): 66.3891
Level 1 (SRSA, SRSAN) : 58.2621
Match %tage for VCF file B
Level 2 (SRSA, SRSAN, SRDA, SRDNA) : 62.6568
Level 1 (SRSA, SRSAN) : 59.8661
Level 3 (SRSA, SRSAN, SRDA, SRDNA, DRDA, DRDNA): 66.3891
Level 2 (SRSA, SRSAN, SRDA, SRDNA) : 64.3818
Match %tage for VCF file B
Level 3 (SRSA, SRSAN, SRDA, SRDNA, DRDA, DRDNA): 68.2168
Level 1 (SRSA, SRSAN) : 59.8661
Matched variants written to match.txt
Level 2 (SRSA, SRSAN, SRDA, SRDNA) : 64.3818
Match logs written to match.log
Level 3 (SRSA, SRSAN, SRDA, SRDNA, DRDA, DRDNA): 68.2168
Matched variants written to match.txt
atks@fantasia:~/data/got2d$ head match.txt
Match logs written to match.log
id1 id2 match_type extended_no_bases normalized
A4 B1 SRSAN 0 1
atks@fantasia:~/data/got2d$ head match.txt
A5 B2 SRSAN 0 1
id1 id2 match_type extended_no_bases normalized
A6 B4 SRSA 0 0
A4 B1 SRSAN 0 1
A7 B5 SRSAN 0 1
A5 B2 SRSAN 0 1
A8 B6 SRSA 0 0
A6 B4 SRSA 0 0
A9 B7 SRDA 0 1
A7 B5 SRSAN 0 1
A10 B8 SRSAN 0 1
A8 B6 SRSA 0 0
A11 B9 SRSAN 0 1
A9 B7 SRDA 0 1
A12 B10 SRSAN 0 1
A10 B8 SRSAN 0 1
A11 B9 SRSAN 0 1
A12 B10 SRSAN 0 1
== Description ==
== Description ==
