File Formats

PED

Describes individuals and their genetic data.

• Space or tab delimited file
• One line for each individual

Columns:

1. Family ID [string]
2. Individual ID [string] – unique, containing only alphanumeric characters
3. Father ID [string]
4. Mother ID [string]
5. Sex [integer] – 1 for female, 2 for male
6. Phenotype [float]
7. SNP1 first allele
8. SNP1 second allele
9. SNP2 first allele
10. SNP2 second allele

More Information

VCF

• meta-information lines
• header line
• data lines (each for a different position in the genome)

Meta-information lines

• start with “##”
• must have ‘‘file format’ field
• ##fileformat=VCFv4.0

###Header line * names the 8 fixed, mandatory columns * tab-delimited

The columns are:

1. #CHROM
2. POS
3. ID
4. REF
5. ALT
6. QUAL
7. FILTER
8. INFO

Data lines

• tab-delimited

Fields:

1. #CHROM: identifier from the reference genome
2. POS: reference position
3. ID: unique identifier like dbSNP rs #
4. REF: A, C, G, T or N, indels include base before event
5. ALT: non-reference alleles called on at least one of the samples; A, C, G, T, N or
6. QUAL: high scores indicate high confidence
7. FILTER: PASS or codes for filters that fail
8. INFO: additional info

More Information

BAM/CRAM

###BAM * binary version of a SAM file * sequence alignment data

###SAM * Header lines start with ‘@’ * Alignment lines have 11 mandatory fields for essential alignment info * More Info

###CRAM * like BAM * compressed version of the alignment * More Info

FASTQ

• stores sequences and Phred qualities
• More Info

23&Me

snp/rs id chrm # position genotype

rs4477212 1 82154 AA rs3094315 1 752566 AG rs3131972 1 752721 AG rs12124819 1 776546 AA