The relationship between QUAL and FQ INFO in mpileup output

My mpileup output looks like this:

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    HS
Chr1    1954    .    G    A    155    .    DP=21;VDB=0.0401;AF1=1;AC1=2;DP4=0,0,13,7;MQ=42;FQ=-87    GT:PL:DP:SP:GQ    1/1:188,60,0:20:0:99
Chr1    23056    .    C    A    169    .    DP=22;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,12,10;MQ=42;FQ=-93    GT:PL:DP:SP:GQ    1/1:202,66,0:22:0:99
Chr1    31071    .    A    G    182    .    DP=31;VDB=0.0333;AF1=1;AC1=2;DP4=0,0,15,15;MQ=42;FQ=-117    GT:PL:DP:SP:GQ    1/1:215,90,0:30:0:99
Chr1    31478    .    C    T    169    .    DP=26;VDB=0.0394;AF1=1;AC1=2;DP4=0,0,15,11;MQ=42;FQ=-105    GT:PL:DP:SP:GQ    1/1:202,78,0:26:0:99
Chr1    33667    .    A    G    172    .    DP=24;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,10,14;MQ=42;FQ=-99    GT:PL:DP:SP:GQ    1/1:205,72,0:24:0:99

Could someone tell me what's the relationship between QUAL and FQ, or how can I get the FQ value if I only have QUAL value?

THANKS A LOT.

snp

• 2,261 views • link

updated 4.7 years ago by Ram

• written 12.0 years ago by mchone69 •

0 answers

No answers yet.

More posts like this

VCFtools alternative to --minDP flags not working?
written 9.7 years ago by beausoleilmo

Since my VCFtools --minDP flag and --maxDP are not working, is there a way to manually code the filtering? vcftools --vcf output.vcf --recode --recode-INFO-all --minDP …
vcftools DP filter error
written 10.0 years ago by sun.nation

I used this command: vcftools --vcf cotton2.all.bcf.vcf --out cotton2.all.bcf.vcf.maf1.vcf \ --remove-filtered-all --max-missing-count 0 --minDP 10 --minQ 10 \ --maxDP 1000 --maf 1.0 --recode --recode-INFO-all to …
VCF file REF column only contains N
written 10.2 years ago by genie66 •

I am using samtools mpileup to call variant. Command used: samtools mpileup -u -f "/gpfs/home/g/o/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa" "/gopisiva/Mason/Single_cell/SC_Stressed/*.bam" | bcftools view -bvcg - > SC_Stressed.raw.bcf" bcftools view …
SNP at every chromosome position
written 10.9 years ago by waqasnayab

Hi, I have SOLiD sequencing data. After aligning with SHRiMP2, I used samtools mpileup for SNP calling: samtools mpileup -C50 -gf hg38.fa -o var.raw.bcf input.bam …
Allele Depth (~ Dp4) Values For All (Including Multi-Allelic Alt) Possible Alleles Reported?
written 12.9 years ago by Rm

Is there a quick way to get allele read depth for all possible alleles say from <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> or mpileup? <pre><code>10 101023 . A G,T …
Why Is The Variant File Produced By Samtools So Large? It Is About ~34G.
written 13.0 years ago by Jordan

Hi, I have a <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> file of size 62G. When I do the variant analysis by <a href='http://samtools.sourceforge.net/'>samtools</a>, it gives a huge bcf file …
Vcf-Tools : Error "Broken Vcf Header, No Column Names?'"
written 13.9 years ago by Pierre Lindenbaum

I've indexed a set of vcf with tabix. <pre><code>$ gunzip -c A.vcf.bgz ##fileformat=VCFv4.1 (...) #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A chr1 …
Extracting Specific Reads From Vcf File
written 14.1 years ago by Bnfoguy •

Hello, I am trying to extract indels with coverage ~1 and they are in a VCF file. How do I write a python script or …
Strand Information On Vcf
written 14.1 years ago by Jirapong •

My mpileup output looks like this. <pre><code>#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT xyzzy.W1g7rI9gs2.bam X 533 . C G 25 . DP=42;VDB=0.0033;AF1=0.5;AC1=1;DP4=20,0,18,0;MQ=20;FQ=26.8;PV4=1,7.1e-22,1,1 GT:PL:GQ …
I Did A Samtools Pileup And Ended In A Vcf Format Like This
written 14.3 years ago by satish.nair •

Hi Everyone I was doing the <a href='http://samtools.sourceforge.net/'>samtools</a> mpileup piping with bcftools using this command ("samtools mpileup -uf hg19.fa SingleCell5.chrM.bam | bcftools view -cg -v …