No informative markers were found.

[Shea Lambert]

Hello,

I am using verifyBamID v. 1.1.3 and get the following error (using --verbose):

Reading 10000 markers from VCF file

Finished reading 14974 markers from VCF file

Total of 0 informative markers passed after AF >= 0.010000 and callRate >= 0.500000 threshold

ERROR : No informative markers were found. Does the VCF have individual genotypes or either AF entry or AC & AN entries included in the INFO field?

However, I can see that my vcf has AF, AC, and AN entries in the INFO field, and I pre-filtered to contain only markers with AF > 0.01 and callrate > 0.5.

This error was recently found in another thread to be caused by a "chr" prefix in the sequence field (https://groups.google.com/forum/#!topic/verifybamid/RlUyqSaBRVo)

In case there could be another parsing error for the sequence field, here's an example header entry for my .bam file:

@SQ SN:occidentalis_paired_contig_354947 LN:4501

Thanks for any advice,

Shea Lambert

[Mary Kate Wing]

Sorry for the delayed response.  Let me know if you have already figured out your issue.

Looking at the code that reads the markers, there are a few checks that exclude the read markers from being included in the number of informative markers:

1) The marker is for a non-autosome.  This should print a warning message the first couple of times it occurs that says:

"Skipping no-autosomal marker <chrom>:<pos>"

It should accept 1-22 or chr1-chr22.

2) AF < minAF which it sounds like shouldn't be happening based on your filter

There aren't any warning messages about this one.  I believe AF is recalculated from AC & AN rather than just using the AF field.

3) callRate < minCallRate which it sounds like shouldn't be happening based on your filter

There aren't any warning messages about this one.

4) Multiple Alternates - only a single alternate is expected.  This should print a warning message:

"Skipping marker <chrom>:<pos> with multiple alternative alleles"

Do you happen to see either of those 2 warning messages?

Attached is an updated version of VerifyBamID.cpp that should print warning messages for the first couple of cases of AF<minAF and callRate<minCallRate, so we can identify if any markers are being excluded unexpectedly due to those reasons.  You can try replacing your copy of VerifyBamID.cpp with this one and typing make to rebuild.

Let me know what you find/see.

Thanks,

Mary Kate

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[Shea Lambert]

Hi Mary Kate,

Thanks very much for your response - sorry it took me so long to get back around to this...

Unfortunately,  using the updated VerifyBamID.cpp, I'm not getting any new error messages. 

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[alison...@my.uri.edu]

Hi,

I am getting the same error. My vcf file has AF entries, but not AC or AN entries (file generated in ANGSD). Is there a way to use the AF entries themselves (which the error message makes it sound like can be used), or do I need to re-generate the vcf in a different way (e.g. GATK)

Thanks!

Alison

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[Hyun Min Kang]

I think it should work with AF field only. Is it not the case?

[alison...@my.uri.edu]

Thanks for your reply - maybe there is something else wrong? I would really appreciate any suggestions!

My command is:

verifyBamID/bin/verifyBamID --vcf ../all_samples_vcf_file.vcf --bam ../all_samples_combined.bam --out all_samples_BamID_initial --verbose --chip-none

The exact error I'm getting is:

Finished reading 185265 markers from VCF file

Total of 0 informative markers passed after AF >= 0.010000 and callRate >= 0.500000 threshold

ERROR : No informative markers were found. Does the VCF have individual genotypes or either AF entry or AC & AN entries included in the INFO field?

Aborted

And the beginning of my VCF file looks like:

-bash-4.1$ head -14 ../all_samples_vcf_file.vcf

##fileformat=VCFv4.2(angsd version)

##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">

##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">

##INFO=<ID=RA,Number=1,Type=String,Description="Reference Allele (included since ANGSD places the MAJOR allele under REF)">

##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">

##INFO=<ID=AF,Number=A,Type=Float,Description="Minor Allele Frequency">

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">

##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the major and minor alleles in the order listed">

##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities">

##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods">

##FORMAT=<ID=GL,Number=G,Type=Float,Description="scaled Genotype Likelihoods (loglikeratios to the most likely (in log10))">

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ind0    ind1    ind2    ind3    ind4    ind5    ind6    ind7    ind8    ind9    ind10   ind11   ind12   ind13   ind14   ind15   ind16   ind17   ind18   ind19   ind20ind21   ind22   ind23   ind24   ind25   ind26   ind27   ind28   ind29   ind30   ind31   ind32   ind33   ind34   ind35   ind36   ind37   ind38   ind39   ind40   ind41   ind42   ind43   ind44   ind45   ind46   ind47   ind48   ind49   ind50ind51   ind52   ind53   ind54   ind55   ind56   ind57   ind58   ind59   ind60   ind61   ind62   ind63   ind64   ind65   ind66   ind67   ind68   ind69   ind70   ind71   ind72   ind73   ind74   ind75   ind76   ind77   ind78   ind79   ind80ind81   ind82   ind83   ind84   ind85   ind86   ind87   ind88   ind89   ind90   ind91   ind92   ind93   ind94   ind95   ind96   ind97   ind98   ind99   ind100  ind101  ind102  ind103

Contig0 40778   .       C       G       .       PASS    NS=101;AF=0.010039      GP:GL   1.000000,0.000000,0.000000:0.000000,-7.525845,-21.002408        1.000000,0.000000,0.000000:0.000000,-9.031014,-21.428737        1.000000,0.000000,0.000000:0.000000,-6.321711,-20.450566     0.999367,0.000633,0.000000:0.000000,-1.505169,-13.786638        1.000000,0.000000,0.000000:0.000000,-7.525845,-21.146823        1.000000,0.000000,0.000000:0.000000,-12.342387,-22.140399       1.000000,0.000000,0.000000:0.000000,-12.041353,-21.882346    1.000000,0.000000,0.000000:0.000000,-14.148590,-22.183237       1.000000,0.000000,0.000000:0.000000,-8.729980,-21.621184        1.000000,0.000000,0.000000:0.000000,-20.169266,-23.326286    1.000000,0.000000,0.000000:0.000000,-16.556861,-22.673606       1.000000,0.000000,0.000000:0.000000,-10.837218,-21.683008       0.999998,0.000002,0.000000:0.000000,-3.913440,-19.063652        1.000000,0.000000,0.000000:0.000000,-19.868233,-23.401781    1.000000,0.000000,0.000000:0.000000,-14.148590,-22.187096       0.980024,0.019875,0.000101:0.000000,0.000000,0.000000   1.000000,0.000000,0.000000:0.000000,-19.567198,-23.386333       1.000000,0.000000,0.000000:0.000000,-7.826879,-20.990596     0.980024,0.019875,0.000101:0.000000,0.000000,0.000000   1.000000,0.000000,0.000000:0.000000,-17.760995,-22.848015       1.000000,0.000000,0.000000:0.000000,-16.556860,-22.499788       0.000000,1.000000,0.000000:-15.925289,0.000000,-18.203711    1.000000,0.000000,0.000000:0.000000,-17.158928,-22.746623       1.000000,0.000000,0.000000:0.000000,-21.284724,-23.994990       1.000000,0.000000,0.000000:0.000000,-10.536184,-21.200542       1.000000,0.000000,0.000000:0.000000,-24.082705,-24.375257    1.000000,0.000000,0.000000:0.000000,-15.051691,-22.342175       1.000000,0.000000,0.000000:0.000000,-15.352725,-22.262935       1.000000,0.000000,0.000000:0.000000,-17.760995,-22.730382    1.000000,0.000000,0.000000:0.000000,-13.847556,-22.207944       1.000000,0.000000,0.000000:0.000000,-18.664098,-23.022005       1.000000,0.000000,0.000000:0.000000,-20.470300,-23.456062       1.000000,0.000000,0.000000:0.000000,-20.169266,-23.355748    1.000000,0.000000,0.000000:0.000000,-18.363063,-23.244325       1.000000,0.000000,0.000000:0.000000,-17.760996,-22.723856       1.000000,0.000000,0.000000:0.000000,-20.397471,-23.925981       1.000000,0.000000,0.000000:0.000000,-7.224812,-21.339528     1.000000,0.000000,0.000000:0.000000,-15.653758,-22.314778       1.000000,0.000000,0.000000:0.000000,-6.923778,-20.792714        1.000000,0.000000,0.000000:0.000000,-15.051691,-22.317384       1.000000,0.000000,0.000000:0.000000,-11.138251,-21.556606    1.000000,0.000000,0.000000:0.000000,-13.546523,-21.966930       1.000000,0.000000,0.000000:0.000000,-16.255826,-22.575015       1.000000,0.000000,0.000000:0.000000,-18.664098,-23.191539    0.999683,0.000317,0.000000:0.000000,-1.806203,-14.936784        1.000000,0.000000,0.000000:0.000000,-9.793110,-21.232249        1.000000,0.000000,0.000000:0.000000,-15.653758,-22.436044       1.000000,0.000000,0.000000:0.000000,-11.740319,-21.752969    0.980024,0.019875,0.000101:0.000000,0.000000,0.000000   1.000000,0.000000,0.000000:0.000000,-16.255826,-22.866661       0.994956,0.005044,0.000000:0.000000,-0.602068,-4.826820 0.999990,0.000010,0.000000:0.000000,-3.311372,-18.583258     1.000000,0.000000,0.000000:0.000000,-18.965131,-23.274524       1.000000,0.000000,0.000000:0.000000,-15.051691,-22.385730       1.000000,0.000000,0.000000:0.000000,-11.439285,-21.711212       1.000000,0.000000,0.000000:0.000000,-21.674435,-23.783340    1.000000,0.000000,0.000000:0.000000,-15.653758,-22.516463       1.000000,0.000000,0.000000:0.000000,-17.459961,-22.799982       1.000000,0.000000,0.000000:0.000000,-9.633083,-21.442969        1.000000,0.000000,0.000000:0.000000,-21.373401,-23.736623    1.000000,0.000000,0.000000:0.000000,-10.235150,-21.519362       0.999960,0.000040,0.000000:0.000000,-2.709304,-17.273692        0.999960,0.000040,0.000000:0.000000,-2.709304,-18.325696     0.999683,0.000317,0.000000:0.000000,-1.806203,-14.287831        1.000000,0.000000,0.000000:0.000000,-14.449623,-21.950409       1.000000,0.000000,0.000000:0.000000,-23.179604,-23.848228       1.000000,0.000000,0.000000:0.000000,-24.985808,-24.787538    1.000000,0.000000,0.000000:0.000000,-17.459961,-22.826871       1.000000,0.000000,0.000000:0.000000,-27.093045,-25.116785       1.000000,0.000000,0.000000:0.000000,-29.200281,-25.612009       1.000000,0.000000,0.000000:0.000000,-14.449623,-22.141489    1.000000,0.000000,0.000000:0.000000,-21.674435,-23.665488       1.000000,0.000000,0.000000:0.000000,-20.169266,-23.661356       1.000000,0.000000,0.000000:0.000000,-25.587875,-24.881001       1.000000,0.000000,0.000000:0.000000,-25.587875,-24.836682    1.000000,0.000000,0.000000:0.000000,-19.567198,-23.248018       1.000000,0.000000,0.000000:0.000000,-19.567198,-23.288988       1.000000,0.000000,0.000000:0.000000,-20.169266,-23.172173    1.000000,0.000000,0.000000:0.000000,-31.307516,-26.291467       1.000000,0.000000,0.000000:0.000000,-18.664098,-23.165923       1.000000,0.000000,0.000000:0.000000,-10.837218,-21.771576       1.000000,0.000000,0.000000:0.000000,-21.373401,-23.662761    1.000000,0.000000,0.000000:0.000000,-9.332049,-21.483194        1.000000,0.000000,0.000000:0.000000,-16.556860,-22.873468       1.000000,0.000000,0.000000:0.000000,-11.439285,-21.728433       1.000000,0.000000,0.000000:0.000000,-8.428947,-20.959189     1.000000,0.000000,0.000000:0.000000,-10.966910,-21.707472       0.989962,0.010038,0.000000:0.000000,-0.301034,-3.800000 1.000000,0.000000,0.000000:0.000000,-5.117575,-20.342397        0.999995,0.000005,0.000000:0.000000,-3.612406,-18.420592     0.000000,1.000000,0.000000:-15.416278,0.000000,-13.498525       0.999995,0.000005,0.000000:0.000000,-3.612406,-19.542273        1.000000,0.000000,0.000000:0.000000,-12.643420,-22.036821   0.999995,0.000005,0.000000:0.000000,-3.612406,-19.263411 0.998734,0.001266,0.000000:0.000000,-1.204135,-10.930684        1.000000,0.000000,0.000000:0.000000,-16.857895,-22.601469       1.000000,0.000000,0.000000:0.000000,-4.816541,-20.278043     1.000000,0.000000,0.000000:0.000000,-11.439285,-21.945894       1.000000,0.000000,0.000000:0.000000,-19.567198,-23.331297       0.989957,0.010038,0.000005:0.000000,-0.301034,-1.300000 0.999990,0.000010,0.000000:0.000000,-3.311372,-19.144838     0.999999,0.000001,0.000000:0.000000,-4.214473,-19.565483        1.000000,0.000000,0.000000:0.000000,-11.740319,-21.838542       1.000000,0.000000,0.000000:0.000000,-13.245488,-21.924573

[Hyun Min Kang]

Your chromosome names do not match between VCF and BAM.