Answers.Body: <p>You can do the extraction part with the GATK tool VariantsToTable, as described here:</p>
  
  <p><a href="https://gatk.broadinstitute.org/hc/en-us/articles/360041414592-VariantsToTable" rel="nofollow noreferrer">https://gatk.broadinstitute.org/hc/en-us/articles/360041414592-VariantsToTable</a></p>
  
  <p>The usage example from that doc: </p>
  
  <pre><code>gatk VariantsToTable \
      -V input.vcf \
      -F CHROM -F POS -F TYPE -GF AD \
      -O output.table
  </code></pre>
  
  <p>would produce a file that looks like:</p>
  
  <pre><code> CHROM  POS        TYPE   HSCX1010N.AD  HSCX1010T.AD
   1      31782997   SNP    77,0          53,4
   1      40125052   SNP    97,0          92,7
   1      65068538   SNP    49,0          35,4
   1      111146235  SNP    69,1          77,4
  </code></pre>
  
  <p>So you might still need to reorder columns etc but that should allow you to at least get the values out in a tabular format that will be easier to work with.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-23T20:19:53.937Z
Answers.LastActivityDate: 2020-04-23T20:19:53.937Z
Answers.UserDisplayName: Geraldine_VdAuwera
Answers.Body: <p>To extract the DP fields from a VCF file, you could use a tool like <a href="https://www.htslib.org/doc/bcftools.html#query" rel="nofollow noreferrer"><code>bcftools query</code></a>:</p>
  
  <blockquote>
    <p>Extracts fields from VCF or BCF files and outputs them in user-defined format.</p>
  </blockquote>
  
  <p>You could start from something like this:</p>
  
  <pre><code>bcftools query -Hf 'CHC2432T\t%TYPE\t%CHROM\t%POS\t%REF\t%ALT[\t%DP]\n' file.vcf
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-13T08:13:38.617Z
Answers.Text: Sorry, how I can add RU=TAC part to tumour sample?
Answers.UserDisplayName: Zizogolu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-12T19:27:27.120Z
Answers.LastActivityDate: 2019-04-12T19:27:27.120Z
Answers.UserDisplayName: Jukka Matilainen
Body: <p>I have a .vcf file</p>
  <p><a href="https://www.dropbox.com/s/8v73nppwg3a1tnd/LP2000109-DNA_A01_vs_LP2000103-DNA_A01.SVannotated.txt?dl=0" rel="nofollow noreferrer">https://www.dropbox.com/s/8v73nppwg3a1tnd/LP2000109-DNA_A01_vs_LP2000103-DNA_A01.SVannotated.txt?dl=0</a></p>
  <p>with this header</p>
  <pre><code>##startTime=Fri Mar 29 16:46:32 2019
  #CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NORMAL  TUMOR
  1   54586   .   T   C   .   PASS    DP=39;MQ=50.55;MQ0=0;NT=ref;QSS=48;QSS_NT=48;ReadPosRankSum=1.92;SGT=TT-&gt;CT;SNVSB=0.00;SOMATIC;SomaticEVS=10.83;TQSS=1;TQSS_NT=1    AU:CU:DP:FDP:GU:SDP:SUBDP:TU    0,0:0,0:20:0:0,0:0:0:20,20  0,0:6,6:18:0:0,0:0:0:12,13
  1   103241  .   C   T   .   PASS    DP=120;MQ=24.94;MQ0=35;NT=ref;QSS=47;QSS_NT=47;ReadPosRankSum=2.09;SGT=CC-&gt;CT;SNVSB=0.00;SOMATIC;SomaticEVS=9.44;TQSS=2;TQSS_NT=2   AU:CU:DP:FDP:GU:SDP:SUBDP:TU    0,1:32,47:33:1:0,0:0:0:0,5  0,
  </code></pre>
  <p>The &quot;DP&quot; field in the vcf shows the depth of the individual samples; So in this file, the first locus has the following format fields:</p>
  <pre><code>AU:CU:DP:FDP:GU:SDP:SUBDP:TU    0,0:0,0:20:0:0,0:0:0:20,20  0,0:6,6:18:0:0,0:0:0:12,13
  </code></pre>
  <p>So according to this (DP field of normal and tumor samples), normal sample has a depth of 20 and tumor sample has a depth of 18.</p>
  <p>So how I could extract the read depth for all loci as described for the first position? The desired output would be like this [note that the VCF is taken from my own data but the table is my desired format that I don't know how to get that from my own data. chr have been added manually because my reference genome is hg19]:</p>
  <pre><code>  Sample   Type   CHROM       POS    REF  ALT       Tumor_Depth Normal_Depth
    CHC2432T SNV    chr1  102961055    G    A                  64           62      
    CHC2432T SNV    chr1  105492588    A    T                  66           73     
    CHC2432T SNV    chr1  108628724    C    T                  45           54    
    CHC2432T SNV    chr1  109692113    G    T                  53           29     
    CHC2432T SNV    chr1  109692114    G    T                  53           31     
    CHC2432T SNV    chr1  120676701    T    C                  48           87   
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-12T14:57:25.303Z
Comments.Text: Your vcf file is truncated (see `tail -n1 _double_filtered_013_pre_indels.vcf`). I assume that's just the copy you uploaded to dropbox, but check your actual file to be sure.
Comments.UserDisplayName: terdon
Tags: <vcf><wgs><snv>
Title: Parsing .vcf file for this information
ThreadText: # Parsing .vcf file for this information
  
  (Asked by: username_0 on 2019-04-12)
  
  I have a .vcf file
  
  <https://www.dropbox.com/s/8v73nppwg3a1tnd/LP2000109-DNA_A01_vs_LP2000103-DNA_A01.SVannotated.txt?dl=0>
  
  with this header
  
  ```
  ##startTime=Fri Mar 29 16:46:32 2019
  #CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NORMAL  TUMOR
  1   54586   .   T   C   .   PASS    DP=39;MQ=50.55;MQ0=0;NT=ref;QSS=48;QSS_NT=48;ReadPosRankSum=1.92;SGT=TT->CT;SNVSB=0.00;SOMATIC;SomaticEVS=10.83;TQSS=1;TQSS_NT=1    AU:CU:DP:FDP:GU:SDP:SUBDP:TU    0,0:0,0:20:0:0,0:0:0:20,20  0,0:6,6:18:0:0,0:0:0:12,13
  1   103241  .   C   T   .   PASS    DP=120;MQ=24.94;MQ0=35;NT=ref;QSS=47;QSS_NT=47;ReadPosRankSum=2.09;SGT=CC->CT;SNVSB=0.00;SOMATIC;SomaticEVS=9.44;TQSS=2;TQSS_NT=2   AU:CU:DP:FDP:GU:SDP:SUBDP:TU    0,1:32,47:33:1:0,0:0:0:0,5  0,
  
  ```
  
  The "DP" field in the vcf shows the depth of the individual samples; So in this file, the first locus has the following format fields:
  
  ```
  AU:CU:DP:FDP:GU:SDP:SUBDP:TU    0,0:0,0:20:0:0,0:0:0:20,20  0,0:6,6:18:0:0,0:0:0:12,13
  
  ```
  
  So according to this (DP field of normal and tumor samples), normal sample has a depth of 20 and tumor sample has a depth of 18.
  
  So how I could extract the read depth for all loci as described for the first position? The desired output would be like this [note that the VCF is taken from my own data but the table is my desired format that I don't know how to get that from my own data. chr have been added manually because my reference genome is hg19]:
  
  ```
    Sample   Type   CHROM       POS    REF  ALT       Tumor_Depth Normal_Depth
    CHC2432T SNV    chr1  102961055    G    A                  64           62      
    CHC2432T SNV    chr1  105492588    A    T                  66           73     
    CHC2432T SNV    chr1  108628724    C    T                  45           54    
    CHC2432T SNV    chr1  109692113    G    T                  53           29     
    CHC2432T SNV    chr1  109692114    G    T                  53           31     
    CHC2432T SNV    chr1  120676701    T    C                  48           87   
  
  ```
  
  **Tags:** vcf, wgs, snv
  
  > **Comments:**
  > **username_1**: Your vcf file is truncated (see `tail -n1 _double_filtered_013_pre_indels.vcf`). I assume that's just the copy you uploaded to dropbox, but check your actual file to be sure.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2020-04-23. Score: 1
  
  You can do the extraction part with the GATK tool VariantsToTable, as described here:
  
  <https://gatk.broadinstitute.org/hc/en-us/articles/360041414592-VariantsToTable>
  
  The usage example from that doc:
  
  ```
  gatk VariantsToTable \
      -V input.vcf \
      -F CHROM -F POS -F TYPE -GF AD \
      -O output.table
  
  ```
  
  would produce a file that looks like:
  
  ```
   CHROM  POS        TYPE   HSCX1010N.AD  HSCX1010T.AD
   1      31782997   SNP    77,0          53,4
   1      40125052   SNP    97,0          92,7
   1      65068538   SNP    49,0          35,4
   1      111146235  SNP    69,1          77,4
  
  ```
  
  So you might still need to reorder columns etc but that should allow you to at least get the values out in a tabular format that will be easier to work with.
  
  
  ---
  
  ### Answer by username_3 on 2019-04-12. Score: 1
  
  To extract the DP fields from a VCF file, you could use a tool like [`bcftools query`](https://www.htslib.org/doc/bcftools.html#query):
  
  > Extracts fields from VCF or BCF files and outputs them in user-defined format.
  
  You could start from something like this:
  
  ```
  bcftools query -Hf 'CHC2432T\t%TYPE\t%CHROM\t%POS\t%REF\t%ALT[\t%DP]\n' file.vcf
  
  ```
  
  > **Comments:**
  > **username_0**: Sorry, how I can add RU=TAC part to tumour sample?  
  
  ---
  
  