results from SNPSift Concordance
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4.1 years ago
Apoorva ▴ 310

Hi everyone,

I have multiple samples that were sequenced and subsequently genotyped. I want to find potential mismatches by comparing the two experiments. I called snp's using VarScan and then used SNPSift concordance. I have some trouble understanding what the results mean. The concordance by variance were not hard to understand. But the concordance by sample is confusing.

Following is the results from summary.txt

Number of samples:
5   File genotype.vcf
5   File sequencing.vcf
5   Both files

Errors:
REF fields does not match   3
ALT field does not match    62

I transposed the concordance_by_summary.txt for easy viewing

sample  samp1   samp2   samp3   samp4   samp5
MISSING_ENTRY_genotype.MISSING_ENTRY_sequencing 0   0   0   0   0
MISSING_ENTRY_genotype.MISSING_GT_sequencing    25186   21172   24599   23377 17533
MISSING_ENTRY_genotype.REF  0   0   0   0   0
MISSING_ENTRY_genotype.ALT_1    1950    3731    2160    2737    6039
MISSING_ENTRY_genotype.ALT_2    3224    5457    3601    4246    6788
MISSING_GT_genotype.MISSING_ENTRY_sequencing    5740110 5820568 5803803 5761099 5811924
MISSING_GT_genotype.MISSING_GT_sequencing   27360   26483   26457   24585   16087
MISSING_GT_genotype.REF 0   0   0   0   0
MISSING_GT_genotype.ALT_1   194 265 319 360 674
MISSING_GT_genotype.ALT_2    59  69  63  99 195
REF.MISSING_ENTRY_sequencing    0   0   0   0   0
REF.MISSING_GT_sequencing   0   0   0   0   0
REF.REF 0   0   0   0   0
REF.ALT_1   0   0   0   0   0
REF.ALT_2   0   0   0   0   0
ALT_1.MISSING_ENTRY_sequencing  4748629 4630439 4657942 4714946 4655508
ALT_1.MISSING_GT_sequencing 22123   19498   20188   17694   13286
ALT_1.REF   0   0   0   0   0
ALT_1.ALT_1  6004    7926    7401   10962   18038
ALT_1.ALT_2  811    1048    1008    1343    2711
ALT_2.MISSING_ENTRY_sequencing  3109366 3147098 3136360 3122060 3130673
ALT_2.MISSING_GT_sequencing 25032   23773   23969   19992   13804
ALT_2.REF   0   0   0   0   0
ALT_2.ALT_1 132 215 197 233 444
ALT_2.ALT_2  5371    7809    7484   11818   21847
ERROR   65  65  65  65  65

I understand the ERROR=65 is the num of REF fields and ALT fields (3+62) that dont match. But I don't understand which sample(s) it is from. Also, does SNPSift compare samples with each other ?

SNPSift concordance snp • 1.6k views
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