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bcftools filtering INFO column issues (empty output)
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Entering edit mode
14 months ago
Molly_K • 50
United States

How can I filter out variants with R2!="." in the INFO column?

bcftools view -i 'INFO/R2!="."' -Oz $FILE -o $OUTFILTERED

The above generated a vcf.gz file with only the header.

I have used the same command line to filter VCF file based on the R2 score and it worked fine. Just wondering what is missing here that I don't get any output after filtering?


Here's more detailed information if you are interested. I filtered the R2 score after imputation using bcftools, then used vcftools to remove specific individuals, however, vcftools split multiallelic sites so there are rows without R2 score. The downstream analyses I am using is the DosageConvertor, which requires the R2 information.


bcftools view -e '(R2<0 || R2>=0)' chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz | head -19

##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##filedate=2018.11.9
##source=Minimac3
##contig=<ID=22>
##FILTER=<ID=GENOTYPED,Description="Marker was genotyped AND imputed">
##FILTER=<ID=GENOTYPED_ONLY,Description="Marker was genotyped but NOT imputed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="Estimated Alternate Allele Dosage : [P(0/1)+2*P(1/1)]">
##FORMAT=<ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and 1/1">
##INFO=<ID=AF,Number=1,Type=Float,Description="Estimated Alternate Allele Frequency">
##INFO=<ID=MAF,Number=1,Type=Float,Description="Estimated Minor Allele Frequency">
##INFO=<ID=R2,Number=1,Type=Float,Description="Estimated Imputation Accuracy">
##INFO=<ID=ER2,Number=1,Type=Float,Description="Empirical (Leave-One-Out) R-square (available only for genotyped variants)">
##bcftools_viewVersion=1.9+htslib-1.9
##bcftools_viewCommand=view -i 'INFO/R2 > 0.4' -Oz -o /home/chr22_rsq_filtered.vcf.gz /home/chr22.dose.vcf.gz; Date=Tue Nov 13 11:51:58 2018
##bcftools_viewCommand=view -e '(R2<0 || R2>=0)' chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz; Date=Wed Nov 28 13:29:28 2018
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  11784   9448    10003420    15472   10004782    10008417    10013040    19706   10010631    10011283    10012586    21206   21331   10903   7245    26461   19614   29232   10009360    9769    10010684    11365   13165   15117   2220    10006632    5607    10013521    22310   21492   10012059    10013319    17865   32454   15736   36987   17374   18284   27381   28469   34892   38216   12431   15518   10013520    10005321    11712   10009688    10008150    10002649    5636    4016    2319    15598   12784   10008181    33183   17191   16638   10004678    9663    24877   40681   33313   10000724    12484   9694    977 9752    8875    11258   10010739    10005063    10009709    22920   11089   10000267    11114   27787   18302   34238   18528   18252   13698   22380   35748   35622   35901   10010241    10001457    10010552    10008477    10010189    14321   10011307    10008227    14149   13863   15355   15028   10003971    10001660    20541   27937   23084   21668   10006375    10013305    10007238    10012905    10012018    3561    3579    12362   100013910007005 10011320    10007334    10007731    10008955    10000728    10003319    10003342    10008459    10008003    10006200    10012133    10012276    10000531    10005851    10006611    10012678    22569   17213   24159   10003789    10001994    10007567    803 10000908    10011711    10001612    10001655    10001895    10009034    10009661    10007125    10001236    10001147    10011709    10010519    10010534    10010939    5623    10010473    10002558    10001012    10008536    10007207    100066310003886 10004177    10004145    15131   509 10003452    5648    6340    11710   10868   26833   27020   14488   2372    10803   16171   10000051    10013524    10009852    10012710    10009106    10009604    12280   11420   490 10000542    10009464    10006058    10012203    10011005    26821   10003499    10003867    10002130    10005764    10007018    10005870    10004760    10011645    10011492    10010801    16886   32744   10001309    6335    10003562    10006612    10005023    10007903    10000929    10008048    10608   10012425    10012597    10005211    10005601    10005216    23199   12970   39819   36561   10011522    38108   8102    5223    9469    36338   26681   23585   10000337    10007488    100083010006039 32018   10007070    10011635    31753   10009658    10002325    10008960    10002904    27978   28062   16717   20316   21109   20926   10006048    10004629    5580    13617   33114   10010797    10003512    10000426    10009060    10007611    10002006    10007869    11601   10010407    10010504    10009190    10004334    10004872    14675   14121   12378   20865   20620   36557   10010674    10001912    27209   13447   24725   12201   10003216    10000244    10003199    10002793    10004249    10000013    10008067    31881   10012837    10003500    10010309    13741   10006974    10009990    39732   16789   16431   10010230    10004136    10007568    10010859    10012720    10011862    10003148    10003214    10003187    11476   7874    8521    10012881    8943    21359   7446    32606   21484   10003729    21241   19659   18649   18052   16976   339 22111   5021    22456   100087110009133 10012368    10012435    10003227    15108   10012818    10013497    13708   26469   10533   36149   10004212    10006972    21997   12807   28243   19275   7619    10001475    10007538    10002767    10006290    10007388    10011253    10010756    10000274    10006647    10005810    10006185    4992    2175    11404   11786   14915   13263   16445   16347   16813   10011693    13347   22291   18895   20495   20697   20842   10010541    25576   15932   11991   12063   12707   10003189    859 829 8292    10009906    10001547    10008374    10008437    10008986    10004717    10005306    10006195    10011881    10011760    10010392
22  16578328    22:16578328 A   G   .   PASS    .   GT:DS:GP    0|0:0.033:0.968,0.032,0 1|0:0.812:0.201,0.786,0.013 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.967,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.967,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.967,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.031:0.969,0.031,0 0|0:0.031:0.969,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.967,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.969,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.031:0.969,0.031,0 0|1:0.811:0.201,0.786,0.012 0|0:0.033:0.968,0.032,0 0|0:0.031:0.969,0.031,0 1|0:0.808:0.205,0.782,0.013 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|1:0.808:0.205,0.783,0.012 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.969,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.969,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.967,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.967,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.967,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|1:0.809:0.204,0.783,0.013 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|1:0.808:0.205,0.783,0.013 1|1:1.583:0.043,0.33,0.627  0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.031:0.969,0.031,0 0|1:0.808:0.204,0.783,0.012 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.967,0.032,0 1|0:0.808:0.204,0.783,0.012 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,00|0:0.032:0.968,0.032,0  0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,00|0:0.033:0.968,0.032,0  0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.031:0.969,0.031,0 0|1:0.808:0.204,0.783,0.013 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.031:0.969,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.031:0.969,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.969,0.031,0 0|0:0.031:0.969,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.031:0.969,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.969,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.969,0.031,0 0|0:0.031:0.969,0.031,0 0|0:0.033:0.968,0.032,0 0|1:0.809:0.204,0.783,0.013 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 1|0:0.81:0.203,0.784,0.013  0|0:0.033:0.968,0.032,00|0:0.033:0.968,0.032,0  0|0:0.031:0.969,0.031,0 0|0:0.031:0.969,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,00|0:0.031:0.969,0.031,0  0|0:0.031:0.969,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.031:0.969,0.031,00|0:0.032:0.968,0.032,0  0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,00|0:0.032:0.968,0.031,0  0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,00|0:0.033:0.968,0.032,0  0|0:0.032:0.969,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,00|0:0.032:0.968,0.031,0  0|0:0.033:0.967,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.969,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,00|0:0.032:0.968,0.032,0  0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|1:0.812:0.201,0.786,0.013 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 1|0:0.814:0.199,0.788,0.013 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.031:0.969,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|1:0.809:0.204,0.783,0.013 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.967,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,00|0:0.033:0.967,0.032,0  0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.967,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.031:0.969,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,00|0:0.033:0.968,0.032,0  0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,00|0:0.032:0.968,0.032,0  0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 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1|1:1.587:0.043,0.328,0.63  0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.031:0.969,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.031,0 0|0:0.033:0.968,0.032,0 0|0:0.032:0.968,0.032,0 0|0:0.033:0.968,0.032,0 0|0:0.031:0.969,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.968,0.031,0 0|0:0.032:0.969,0.031,0 0|0:0.033:0.968,0.032,0
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Hello Molly_K ,

could you please post a small example of your vcf file (including the header) with variants that should be kept and those that should be removed?

fin swimmer

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Thanks for adding the example. I don't know if this is a copy&paste problem to biostars. But whatever bcftools command I try, I get the error message [E::vcf_parse_format] Incorrect number of FORMAT fields at 22:16578328

Did you receive any messages like this? This would explain why you just get the header.

I've tried to find that wrong number of FORMAT fields, with this:

$ awk -v OFS="\t" '$0 !~ "^#" {for(i=10;i<=NF;i++) { n = split($i, array, ":"); if(n!=3) {print i, $i}}}' input.vcf
173 0|0:0.032:0.968,0.031,00|0:0.032:0.968,0.032,0
181 0|0:0.032:0.968,0.032,00|0:0.033:0.968,0.032,0
242 0|0:0.033:0.968,0.032,00|0:0.031:0.969,0.031,0
250 0|0:0.031:0.969,0.031,00|0:0.032:0.968,0.032,0
258 0|0:0.032:0.968,0.032,00|0:0.032:0.968,0.031,0
266 0|0:0.032:0.968,0.031,00|0:0.033:0.968,0.032,0
274 0|0:0.032:0.968,0.032,00|0:0.032:0.968,0.031,0
282 0|0:0.032:0.968,0.032,00|0:0.032:0.968,0.032,0
307 0|0:0.033:0.968,0.032,00|0:0.033:0.967,0.032,0
315 0|0:0.032:0.968,0.032,00|0:0.033:0.968,0.032,0
323 0|0:0.032:0.968,0.031,00|0:0.032:0.968,0.032,0
331 0|0:0.031:0.969,0.031,00|0:0.033:0.968,0.032,0
339 0|0:0.032:0.968,0.032,00|0:0.032:0.968,0.032,0
347 0|0:0.032:0.968,0.031,00|0:0.032:0.968,0.031,0
355 0|0:0.033:0.968,0.032,00|0:0.032:0.969,0.031,0

The first column shows you the column number in the vcf file with wrong number of fields, the second column shows you how the wrong column looks like.

fin swimmer

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I apologize for the weird behaviour of the file. I think after copy paste from the terminal there are some tabs missing.

Here's a link to the first 100 rows of the vcf file that I extracted

bcftools view $FILE/chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz | head -100 > $FILE/test2.vcf

https://www.dropbox.com/s/l4ic8bb1mwaf2qo/test2.vcf?dl=0

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Hello again,

in this example file there are no variants that have a R2 value in the INFO column. So after filtering with bcftools view -i 'INFO/R2!="."' you will get of course just the header as no variant fulfill the criteria.

fin swimmer

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can you try

bcftools view -e '(R2<0 || R2>=0)'
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Hi Pierre, here's the output [filter.c:2278 filters_init1] Error: the tag "GQ_MEAN" is not defined in the VCF header

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I meant 'R2', fixed

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Updated the original post to fit in the first 19 rows. It's the header + the first snp. If I don't limit the row number, it would keep running till the end of the file. Thanks.

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Hi Pierre, I used the following command line and noticed a drop in the row numbers

bcftools view -e '(R2<0 || R2>=0)' $FILE/chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz > test1.vcf

wc -l chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz
1176573 chr22_rsq_filtered.vcf_remove12.gz.recode.vcf.gz
wc -l test1.vcf
309798 test1.vcf
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