Line 19: |
Line 19: |
| == 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 == |