[aforntacc]

Those fields will be determined by what ever analysis package you used to generate your vcf file

Some of them might be standard fields which are all explained in the VCF documentation
http://www.1000genomes.org/wiki/Anal...mat-version-41

thanks a lot laura
i am only interested in the difference among the wt and mt, from which i will select candidate regions. i am more than happy if you can point me towards the right direction, this is my very first time handling this kind of data.
thanks

[laura]

Those fields will be determined by what ever analysis package you used to generate your vcf file

Some of them might be standard fields which are all explained in the VCF documentation

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

[aforntacc]

What aspects of the format are you struggling with

The genotypes are shows as index values on the Ref/Alt columns so in your case T is 0 and C is 1

This gives you your give genotypes for this site being T/C, C/C, C/C, T/C, T/C, T/C

Ok, thank you very much, at first i was reluctant to analyse this part of the data but when i saw the previous threads on this website i was encouraged so thanks once again.

Please what use are these (AltSup AC1=12;AF1=1;DP4=0,0,1,1;DP=66;FQ=-26.9;MQ=39;MfGt=0/1;MinDP=0;NeqMfGt=2) for my analysis since i am only interested on the SNPs and INDELS that pass the filtering criteria and their differences among my libararies and not the Reference.
secondly the way you interpreted the GT index is it ture for all sites that pass the quality craiteria.
thank you

[laura]

What aspects of the format are you struggling with

The genotypes are shows as index values on the Ref/Alt columns so in your case T is 0 and C is 1

This gives you your give genotypes for this site being T/C, C/C, C/C, T/C, T/C, T/C

[aforntacc]

Hello every one please i need help i am struggling to understand what to do on my analysis, i have VCF format data on variant call
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 110506_SN132_A_s_1_seq 110506_SN132_A_s_2_seq_ 110506_SN132_A_s_3_seq 110506_SN132_A_s_4_seq_ 110616_SN365_A_s_5_seq_ 110616_SN365_A_s_6_seq_
chr1 11433 . T C 11.4 AltSup AC1=12;AF1=1;DP4=0,0,1,1;DP=66;FQ=-26.9;MQ=39;MfGt=0/1;MinDP=0;NeqMfGt=2 GT:PL: DP:SP:GQ 0/1:0,0,0:0:0:3 1/1:29,3,0:1:0:5 1/1:15,3,0:1:0:5 0/1:0,0,0:0:0:3 0/1:0,0,0:0:0:3 0/1:0,0,0:0:0:3
i have a 6 genotype information corresponding to 1-3 wildtype and 4-6 mutant libraries). i have read the vcf documentations but still struggling to understand my data because i want to compare the difference between WT and MT.
thanks

[wanguan2000]

GQ The Genotype Quality calculation

chr1 10740313 . A G 188.30 PASS AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;HRun=1;Haplotype Score=6.9635;MQ=26.82;MQ0=0;QD=17.12;SB=-72.04;sumGLbyD=20.12 GT:AD: DP :GQ:PL 1/1:1,10:7:21.05:221,21,0

Here PL is 221,21,0

according to samtools mpileup page

PL means SAMtools/BCFtools writes genotype likelihoods in the PL format which is a comma delimited list of phred-scaled data likelihoods of each possible genotype.

P(D|AA) = 10^(-2.21) = 0.006
P(D|AG) = 10^(-0.21) = 0.617
P(D|GG) = 10^(0) = 1

so does it means genotype is GG for this SNP?

And thanks for AD and DP, now i understood it.

GQ:21.05
PL:221,21,0
you had made a calculation error.

P(D|AA) = 10^(-22.1) = 7.943282e-23
P(D|AG) = 10^(-2.1) = 0.007943282
P(D|GG) = 10^(0) = 1
1 - 1/(1+7.943282e-23+0.007943282) = 0.007880684
GT= -10*log(0.007880684,10) = 21.03436

[curious_mapper]

Hi!

I have the following PL's

REF=A
ALT=C,G

PL=159,39,137,0,6,137

P(D|AA)=10^{-15.9}
P(D|AC)=10^{-.39}
P(D|CC)=10^{-13.7}
P(D|AG)=1
P(D|CG)=10^{-0.06}
P(D|GG)=10^{-13.7}

From where I assumed the genotype would be AG, however, looking at the alignment:
A CCCgCcCCcCCCCCCCccccc

I would think it is AC instead, is the order of the genotypes calculated in a different way?
How do I assign the order for:
REF=G
ALT=T,C,A
PL:236,157,228,235,0,131,138,225,224,232

Thanks!

Hi marcela,

I don't know if you were able to figure this out, but I thought I'd write down the order as an exercise.

GG,GT,TT,GC,TC,CC,GA,TA,CA,AA

Karthik

[curious_mapper]

Thanks marcela, but my vcf file doesn't seem to have the AD tag information. I called the SNPs using samtools mpileup on the CLC generated alignments. Is that information suppressed somewhere while generating the SNPs?

Here is an example SNP from the vcf file:

BACT_1513|gi|293366021|ref|NZ_GG749271.1| 97966 . C A,G,T 66 . DP=35;VDB=0.0042;AF1=1;AC1=2;DP4=0,0,7,25;MQ=31;FQ=-82 GT:PL:GQ 1/1:182,138,83,107,0,82,125,29,14,107:99

[marcela]

Hi there!

I guess you can have that info from the BaseCounts or AD:

chr1 724189 . G A 52.24 .

AB=0.500
AC=1
AF=0.50
AN=2
BaseCounts=3,0,3,0
BaseQRankSum=-1.537
DB
DP=6
QD=8.71 . . .

GT:AD: DP:GQ:PL 0/1:3,3:6:82.23:82,0,105

If you don't have this info, you could annotate your SNVs with GATK

[curious_mapper]

Hi,

In the old pileup file of pileup command we could calculate or at least see the allele composition of reads at each position. For instance, if ref base is A and the reads are ......,,,,,,.T.... was meaning 18 A and one T in the reads.

How can we get the same information in VCF file? It is useless to have the Depth but not knowing what is what?

Hi ashrafi_h

Did you find an answer for your question? I stumbled upon this post looking to understand vcf file in detail and am exactly looking on how to get the allele composition frequency information from the vcf file.

[swbarnes2]

Hi,

In the old pileup file of pileup command we could calculate or at least see the allele composition of reads at each position. For instance, if ref base is A and the reads are ......,,,,,,.T.... was meaning 18 A and one T in the reads.

How can we get the same information in VCF file? It is useless to have the Depth but not knowing what is what?

The DP4 value tells you how many high quality reads, across all samples in the vcf
1) match reference, in the forward direction
2) match reference, in the reverse direction
3) match alternate, in the forward direction
4) match alternate, in the reverse direction

The DP includes all the reads, and the DP4 filters poor quality ones, so the sum of the DP4 can be less than the DP value.

[ashrafi_h]

VCF file Allele composition

Hi,

In the old pileup file of pileup command we could calculate or at least see the allele composition of reads at each position. For instance, if ref base is A and the reads are ......,,,,,,.T.... was meaning 18 A and one T in the reads.

How can we get the same information in VCF file? It is useless to have the Depth but not knowing what is what?

Bovine snps in vcf format

Hi Ketan/everyone,

I'm just wondering could anybody point me in the direction of known bovine SNPs in vcf format??

[marcela]

Hi!

I have the following PL's

REF=A
ALT=C,G

PL=159,39,137,0,6,137

P(D|AA)=10^{-15.9}
P(D|AC)=10^{-.39}
P(D|CC)=10^{-13.7}
P(D|AG)=1
P(D|CG)=10^{-0.06}
P(D|GG)=10^{-13.7}

From where I assumed the genotype would be AG, however, looking at the alignment:
A CCCgCcCCcCCCCCCCccccc

I would think it is AC instead, is the order of the genotypes calculated in a different way?
How do I assign the order for:
REF=G
ALT=T,C,A
PL:236,157,228,235,0,131,138,225,224,232

Thanks!

[blackgore]

Hi ketan,

thanks for your fast response! Unfortunately the AF1 tag is not very informative to me, as it's only for the first ALT allele, and pretty much always 1.0 or 0.5. The AF tag, as I understand it, gives proportional representation of all the called alleles, which is what I'm really after.