Contents casedir input file persdir input file genotyper input file paternity case output file

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Input to and output from DNA•VIEW

1. Two co-ordinated files defining cases and people:
   1. Casedir.txt
   2. Persdir.txt
2. A file or files with genotypic data:
   • Genotyper file

• paternity case output file

CASEDIR.TXT

This file has one record for each case. example of casedir.txt

The records are separated by newline characters. Within a record, each field BEGINS [sic] with a tab. Any quotes in the record will be deleted and ignored on input.

The fields are:

1. Case key-field, numeric. (maximum of 7 digits except that two leading additional digits of 20 are permitted). Leading zeros are ignored.
2. Refcase character string. Can be empty.
3. Maternity? single character. Any of mMyY=maternity, blank or p or P=paternity, k or K=kinship, c or C=crime.
4. Compute race(s) one to six lower-case characters, e.g. cb
5. County character string, may be omitted.
6. Posted? character string, may be omitted

PERSDIR.TXT

Paternity roles	Maternity roles	Crime roles	Kinship roles
M Mother N Mother #2 O Mother #3 C Child D Child #2 E Child #3 A Child #4 B Child #5 Q Child #6 V Child #7 W Child #8 X Child #9 Y Child #10 F Man G Man #2 H Man #3	M Father N Father #2 O Father #3 C Child D Child #2 E Child #3 A Child #4 B Child #5 Q Child #6 V Child #7 W Child #8 X Child #9 Y Child #10 F Woman G Woman #2 H Woman #3	M Victim N Victim #2 O Victim #3 U Unknown V Unknown #2 W Unknown #3 X Unknown #4 Y Unknown #5 C Unknown #6 D Unknown #7 E Unknown #8 A Unknown #9 B Unknown #10 S Suspect T Suspect #2 K Suspect #3	V Victim W Victim #2 M Mother N Mother #2 F Father G Father #2 D Daughter E Daughter#2 S Son T Son#2 U Sibling A Sibling#2 B Sibling#3 C Sibling#4 H Half-Sib I Half-Sib#2 X Other Y Other #2 Z Other #3 R Other #4 O Other #5 P Spouse Q Spouse #2 J Pers Item K Pers Item #2 L Pers Item #3
Note: For most kinds of analysis the role names are arbitrary and the various roles have no functional distinction. The exception is thePaternity Case calculate report option, which treats M as stipulated parent, C, D, etc as children to be tested in trios, and F (and G, H) as putative parent.
Role letters and role names for the various genres of cases.

This file has one record several records for each case, one per person. There can be from zero to 26 people in a case. The normal number is three if the case is a paternity case. example of persdir.txt

The records are separated by newline characters. Within a record, each field BEGINS with a tab. Any quotes in the record are deleted and ignored on input.

The records are:

1. Case key-field, numeric. see above
2. Role key-field, character. Any upper-case letter is allowable as a role letter. However, it is preferable to use the standard letters documented in the table to the right, which are slightly different for crime, paternity, and kinship cases (field 3 of casedir). (They are "preferred" only in that DNAVIEW, recognizing them, will mention the name in the 2nd column when displaying the case definition (e.g. M Mother). The 2nd column name has no meaning though; the user is free, for example, to assign grandfathers and uncles to the roles M and D.)
3. Name character string.
4. Person character: 6-9 digit number, last 5 digits may not be all 0, first 4 digits may not all be zero.
5. Draw date date in the Oracle format YYYY/MM/DD e.g. 2001/12/31
6. Race one lower case letter – e.g. c (for Caucasian or whatever arbitrary assignment the user chooses). The code should be omitted or the special code dash (-) for children, for unknowns, or for anyone whose DNA types are of no statistical interest for eventual allele frequency estimation.
7. Growth (undefined), may be omitted
8. Expansion (undefined), may be omitted
9. Adr1 address, may be omitted. Only used by PATER.
10. Adr2 address, may be omitted. Only used by PATER.
11. Adr3 address, may be omitted. Only used by PATER.
12. Adr4 address, may be omitted. Only used by PATER.
13. Adr5 address, may be omitted. Only used by PATER.

GENOTYPER.TXT

This file has one record person, two or more fields per locus, and an additional field called Sample Info. example of genotyper file

The records are separated by newline characters. Within a record, the fields are separated by tabs. The ABI Genotyper software refers to this file as an "allele table."

Sample Info	D3S1358	D3S1358	vWA	vWA	FGA	FGA
16080 M	15	16	14	15	19	21
16080 C	17	18	15	18	19	25
16080 F	16	17	18	18	20	23
2002-00123	15	16	15	20	23	26
etc . . .

Notes:

• Options for the Sample Info are explained in Newsletter 16. Briefly:
  • character string
  • can be in either of two different formats:
    1. Person number in the format nnnn-nnnnn, OR
    2. Case-id + role-in-case i.e. 16080 M stands for the M (mother) of case 16080. Note that this format requires that the case be defined.
• Some variations are allowed for the locus column headings –
  • Several columns may be presented with identical names.
  • A trailing index 1, 2, etc. can be added as the Genotyper does.
  • Column headings after the first can be omitted for a locus. (If a column heading is left empty, it is treated as a repetition of the preceding column heading.)

Paternity Case output file

Paternity Case calculate report can produce an ASCII comma-delimited file with the essential results of the paternity computation. The file name is user-specified. The same file may include several cases. It will include all the "sub-cases" of each case. (A sub-case arises when there are multiple men or multiple children. Each mother-child-man combination comprises a subcase.)

The sample file exemplifies the fields below. Note that there is one record per case-man-child-locus – i.e. 13 records for a trio analyzed with 13 loci.

1. CASE key field, numeric
2. Subcase key field, numeric
3. Probe or locus key field, numeric
4. Enzyme key field, numeric
5. Ma1 mother's (man's if a motherless case) first allele. Blank if motherless (fatherless). Note: Allele 9•3 appears as 9ù3.
6. Ma2 mother's second allele. Blank if motherless.
7. Ch1 child's first allele
8. Ch2 child's second allele
9. Oblig1 blank
10. Oblig2 blank
11. Af1 man's first allele
12. Af2 man's second allele
13. x numeric, P(data | paternity)
14. y numeric, P(data | unrelated)
15. b numeric, P(random man not excluded at this locus | mother and child)
16. ProbeName as a character string
17. EnzymeName or "PCR" or "SNP" as a character string
18. PI numeric, the cumulative x/y over all loci for the sub-case
19. excl numeric, the total number of "excluding" loci for the sub-case
20. last rec? either blank, or a period (.) if the last record of the sub-case
21. LabOk blank
22. Okdate blank
23. Oktime blank
24. Colldate blank
25. Colltime blank
26. Compute race character – lower-case letter; the racial code for the population used to compute this locus