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HadrienGHadrienG
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added sam vcf and gff
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‎file_formats.md‎

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@@ -73,19 +73,111 @@ The quality, also called phred scores is the probability that the corresponding
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Phred scores use a logarithmic scale, and are represented by ASCII characters, mapping to a quality usually going from 0 to 40
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Phred Quality Score | Probability of incorrect base call | Base call accuracy
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- | - | -
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10 | 1 in 10 | 90%
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20 | 1 in 100 | 99%
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30 | 1 in 1000 | 99.9%
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40 | 1 in 10,000 | 99.99%
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50 | 1 in 100,000 | 99.999%
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60 | 1 in 1,000,000 | 99.9999%
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| Phred Quality Score | Probability of incorrect base call | Base call accuracy
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| --- | --- | ---
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| 10 | 1 in 10 | 90%
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| 20 | 1 in 100 | 99%
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| 30 | 1 in 1000 | 99.9%
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| 40 | 1 in 10,000 | 99.99%
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| 50 | 1 in 100,000 | 99.999%
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| 60 | 1 in 1,000,000 | 99.9999%
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### the sam/bam format
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From [Wikipedia](https://en.wikipedia.org/wiki/SAM_(file_format)):
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SAM (file format) is a text-based format for storing biological sequences aligned to a reference sequence developed by Heng Li. The acronym SAM stands for Sequence Alignment/Map. It is widely used for storing data, such as nucleotide sequences, generated by Next generation sequencing technologies and usually mapped to a reference.
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The SAM format consists of a header and an alignment section. The binary representation of a SAM file is a BAM file, which is a compressed SAM file.[1] SAM files can be analysed and edited with the software SAMtools.
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The SAM format has a really extensive and complex specification that you can find [here](https://samtools.github.io/hts-specs/SAMv1.pdf)
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In brief it consists in a header section and reads (with other information) in tab delimited format.
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#### Example header section
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```
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@HD VN:1.0 SO:unsorted
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@SQ SN:O_volvulusOVOC_OM1a LN:2816604
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@SQ SN:O_volvulusOVOC_OM1b LN:28345163
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@SQ SN:O_volvulusOVOC_OM2 LN:25485961
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```
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#### Example read
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```
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M01137:130:00-A:17009:1352/14 * 0 0 * * 0 0 AGCAAAATACAACGATCTGGATGGTAGCATTAGCGATGCGACACTGCTTGAACCGTCAAAG FGGFGCFGFFGC8,,@D?E6EFCF,=AEFFGGDGGGADFGG@>FFEGGG:+<7D>AFCFGG YT:Z:UU
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```
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### the vcf format
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the vcf is also a text-based file format. VCF stands for Variant Call Format and is used to store gene sequence variations (SNVs, indels). The format hs been developped for genotyping projects, and is the standard to represent variations in the genome of a species.
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A vcf is a tab-delimited file with 9 columns, described [here](https://samtools.github.io/hts-specs/VCFv4.2.pdf)
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#### VCF Example
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```
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##fileformat=VCFv4.0
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##fileDate=20110705
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##reference=1000GenomesPilot-NCBI37
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##phasing=partial
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##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
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##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
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##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
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##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
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##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
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##FILTER=<ID=q10,Description="Quality below 10">
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##FILTER=<ID=s50,Description="Less than 50% of samples have data">
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##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
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##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2 Sample3
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2 4370 rs6057 G A 29 . NS=2;DP=13;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:52,51 1|0:48:8:51,51 1/1:43:5:.,.
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2 7330 . T A 3 q10 NS=5;DP=12;AF=0.017 GT:GQ:DP:HQ 0|0:46:3:58,50 0|1:3:5:65,3 0/0:41:3
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2 110696 rs6055 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
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2 130237 . T . 47 . NS=2;DP=16;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:56,51 0/0:61:2
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2 134567 microsat1 GTCT G,GTACT 50 PASS NS=2;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
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chr1 45796269 . G C
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chr1 45797505 . C G
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chr1 45798555 . T C
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chr1 45798901 . C T
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chr1 45805566 . G C
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chr2 47703379 . C T
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chr2 48010488 . G A
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chr2 48030838 . A T
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chr2 48032875 . CTAT -
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chr2 48032937 . T C
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chr2 48033273 . TTTTTGTTTTAATTCCT -
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chr2 48033551 . C G
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chr2 48033910 . A T
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chr2 215632048 . G T
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chr2 215632125 . TT -
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chr2 215632155 . T C
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chr2 215632192 . G A
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chr2 215632255 . CA TG
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chr2 215634055 . C T
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```
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### the gff format
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The general feature format (gff) is another text file format. used for describing genes and other features of DNA, RNA and protein sequences. It is the standrad for annotation of genomes.
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A gff file should, as a vcf, conatins 9 columns described [here](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)
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#### Example gff
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```
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##description: evidence-based annotation of the human genome (GRCh38), version 25 (Ensembl 85)
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##provider: GENCODE
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##contact: gencode-help@sanger.ac.uk
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##format: gtf
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##date: 2016-07-15
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chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
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chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
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chr1 HAVANA exon 11869 12227 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
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chr1 HAVANA exon 12613 12721 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
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chr1 HAVANA exon 13221 14409 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
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```

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