Getting matrix of QDs from VCF file
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6.6 years ago
Jautis ▴ 510

Hi, I have a vcf file and I would like to get a site-by-individual matrix of read depths (the DP label) and a second matrix of just the GQ scores.

What is the easiest way to do this? Thanks in advance!

Ex input:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  samp1 samp2
chr1   100  .       C       T       3106.72 SnpCluster      .       GT:AD:DP:GQ:PL  0/0:1,0:1:3:0,3,42      0/0:3,0:3:9:0,9,132
chr1   120  .       C       G       3106.72 SnpCluster      .       GT:AD:DP:GQ:PL 0/1:3,1:4:30:30,0,123   1/1:0,1:1:3:45,3,0

Ex output for DP:

1    3
4    3
vcf snp • 2.0k views
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If you need the stats for just one sample (column), grep -v '#' test.vcf | cut -f10 | awk -F ':' '{print $3"\t"$4}' should do. For statistics over multiple samples, I would write a script to parse out the details, which should be pretty straightforward.

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Hi,I want to know what the "snpcluster" displayed in the "info" column of your vcf file means

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Weird that you would necropost a 6-year old topic for this; but SnpCluster is a default filter in FreeBayes that filters out variants within a certain distance of one another. Typically a mis-modeled indel will show up as multiple mismatches within the same window. This is largely obviated by more modern local-assembly approaches and local realignment, as well as rank-sum annotations for mapping quality or strand direction, which also tend to correlated with "clustered" variants.

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Thank you for your reply´╝ü I am doing RNA-Seq-related research recently. Do you think Freebayes can use transcriptome data for SNV-calling?

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It can - I refer you to https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1863-4 for a detailed discussion.

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I see,Thank you so much!

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