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The VCF file hava not fully output by using HaplotypeCaller

I have done the SNP and Indel calling about 21 samples by HaplotypeCaller, but I found there have some lines only have part of information in the VCFfile. The informations were cut from the middle of individual ,so I can not fun the filter by this VCF. In the picture ,the line 3094 and 3099 shown this problem, and it is not very commom in this table. Please help me to sovle this problem.

Best Answer


  • fengxiao1889fengxiao1889 ChinaMember

    scaffold1 247512 . G GT 5736.93 . AC=9;AF=0.214;AN=42;BaseQRankSum=-1.506;ClippingRankSum=0.000;DP=1641;ExcessHet=7.7275;FS=33.808;InbreedingCoeff=-0.2727;MLEAC=9;MLEAF=0.214;MQ=49.38;MQRankSum=-15.949;QD=9.72;ReadPosRankSum=-5.149;SOR=4.119 GT:AD:DP:GQ:PL 0/1:41,19:60:99:710,0,1726 0/1:45,23:68:99:869,0,1840 0/0:71,0:71:99:0,223,3311 0/0:86,0:86:99:0,265,3960 0/1:35,14:49:99:476,0,1493 0/0:66,0:66:99:0,214,3140 0/1:59,10:69:99:239,0,2489 0/0:81,0:81:99:0,247,3690 0/0:86,0:86:99:0,265,3942 0/0:97,0:97:99:0,313,4644 0/1:57,35:92:99:1415,0,2405 0/0:86,2:88:99:0,184,3879 0/1:
    scaffold1 1909227 . G A 7934.72 . AC=14;AF=0.333;AN=42;BaseQRankSum=5.786;ClippingRankSum=0.000;DP=1584;ExcessHet=1.2047;FS=3.958;InbreedingCoeff=0.1358;MLEAC=14;MLEAF=0.333;MQ=52.20;MQRankSum=-20.564;QD=12.61;ReadPosRankSum=1.207;SOR=0.750 GT:AD:DP:GQ:PL 0/0:101,0:101:99:0,319,4770 0/0:106,0:106:99:0,334,4995 0/1:55,6:61:77:77,0,2417 0/1:50,6:56:98:98,0,2123 0/0:85,0:85:99:0,262,3915 0/1:52,21:73:99:755,0,2285 0/0:73,0:73:99:0,232,3465 0/0:116,0:116:99:0,352,5265 0/1:58,5:63:26:26,0,2546 0/1:54,7:61:99:131,0,2246 0/0:108,0:108:99:0,346,5175 0/1:54,12:66:99:332,0,2357 0/1:49,47:96:99:1862,

  • shleeshlee CambridgeMember, Broadie, Moderator admin

    Hi @fengxiao1889,

    How are you viewing these VCF records? Can you explain further what you mean when you say "it is not very common"? Also, what is the error message you get from the filtering tool?

  • fengxiao1889fengxiao1889 ChinaMember

    @shlee Thank you very much for your reply
    When I finish the HaplotypeCaller calling, I was tring to do the filiter by VariantFiltration. Then I received a error report as following :MESSAGE: Line 3094: there aren't enough columns for line (we expected 9 tokens, and saw 1 ), for input source: /home/guoj/all.raw.snps.indels.vcf
    Next,I checked the line 3094 found that for this line scaffold1 247512 . G GT 5736.93 as I showed in the first comment ,the information was cut off from "184,3879 0/1: " .Same situation occured in line 3099, the next information I showed “scaffold1 1909227 . G A 7934.72 . ” also cuff from “49,47:96:99:1862,“
    what I said it is not very common means that for now I only find this two lines hava problem

  • fengxiao1889fengxiao1889 ChinaMember

    Thank you very much ,and I will do the test as soon as I can

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