Can not deal with vcf file #4
Comments
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Hello!
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@yzongzjnu have you any update regarding this? |
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is this fine? can I close the issue? |
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Hi, I'm having pretty much the same issue - I'm happy to open a new issue if you prefer. My command: and the error: My VCF was generated with Freebayes, filtered with BCFtools and pruned for linkage with PLINK. Any suggestions you have would be greatly appreciated. Cheers |
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Hello! Could you paste the offending record or line? I saw GTs as "./."
…On Thu, May 14, 2020 at 1:39 PM Cooper ***@***.***> wrote:
Hi, I'm having pretty much the same issue - I'm happy to open a new issue
if you prefer.
My command:
glactools vcfm2acf --fai reference.fasta.fai biallelic.snps.vcf.gz >
biallelic.snps.acf
and the error:
SimpleVCF: unable to determine genotype for field=#.# at position: 1:33
Error: GlacParser tried to read 4 bytes but got 0
My VCF was generated with Freebayes, filtered with BCFtools and pruned for
linkage with PLINK.
Any suggestions you have would be greatly appreciated.
Cheers
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Thank you for responding. Here's the line:
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This is strange, as no records have a "." as GT. Could you send me the
first few lines of the file including the header via email please.
…On Thu, May 14, 2020 at 3:30 PM Cooper ***@***.***> wrote:
Thank you for responding. Here's the line:
1 33 1_33 C T 131342 PASS
AB=0.484013;ABP=9.05068;AC=783;AF=0.628606;AN=1298;AO=6505;CIGAR=1X;DP=13284;DPB=13284;DPRA=0.819753;EPP=2317.25;EPPR=72.2722;GTI=117;LEN=1;MEANALT=1;MQM=41.5646;MQMR=33.472;NS=853;NUMALT=1;ODDS=0.00103555;PAIRED=0.79339;PAIREDR=0.528101;PAO=0;PQA=0;PQR=0;PRO=0;QA=236494;QR=189135;RO=6779;RPL=243;RPP=12096.6;RPPR=3587.12;RPR=6262;RUN=1;SAF=4714;SAP=2855.11;SAR=1791;SRF=3494;SRP=17.0023;SRR=3285;TYPE=snp;technology.illumina=1
GT:DP:AD:RO:QR:AO:QA:GL 1/1:1:0,1:0:0:1:38:-3.79727,-0.30103,0
1/1:11:0,11:0:0:11:362:-32.645,-3.31133,0
1/1:7:1,6:1:16:6:186:-15.4907,-0.557485,0
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I have added a condition on seeing a GT and GL as ".", those will be marked
as no data.
I took the file that you send by email and generated ACF using the
following command:
~/Software/glactools/glactools vcfm2acf --onlyGT --fai
TriTrypDB-46_LdonovaniBPK282A1_Genome.fasta.fai check.vcf.gz > check.acf.gz
Let me know if that works for you.
On Thu, May 14, 2020 at 3:42 PM Gabriel Renaud <gabriel.reno@gmail.com>
wrote:
… This is strange, as no records have a "." as GT. Could you send me the
first few lines of the file including the header via email please.
On Thu, May 14, 2020 at 3:30 PM Cooper ***@***.***> wrote:
> Thank you for responding. Here's the line:
>
> 1 33 1_33 C T 131342 PASS
> AB=0.484013;ABP=9.05068;AC=783;AF=0.628606;AN=1298;AO=6505;CIGAR=1X;DP=13284;DPB=13284;DPRA=0.819753;EPP=2317.25;EPPR=72.2722;GTI=117;LEN=1;MEANALT=1;MQM=41.5646;MQMR=33.472;NS=853;NUMALT=1;ODDS=0.00103555;PAIRED=0.79339;PAIREDR=0.528101;PAO=0;PQA=0;PQR=0;PRO=0;QA=236494;QR=189135;RO=6779;RPL=243;RPP=12096.6;RPPR=3587.12;RPR=6262;RUN=1;SAF=4714;SAP=2855.11;SAR=1791;SRF=3494;SRP=17.0023;SRR=3285;TYPE=snp;technology.illumina=1
> GT:DP:AD:RO:QR:AO:QA:GL 1/1:1:0,1:0:0:1:38:-3.79727,-0.30103,0
> 1/1:11:0,11:0:0:11:362:-32.645,-3.31133,0
> 1/1:7:1,6:1:16:6:186:-15.4907,-0.557485,0
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <#4 (comment)>,
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Seems to be working now, thank you Gabriel! Much appreciated. |
Hi,
I used glactools to convert multiple sample vcf file to acf format and finally treemix format
./glactools vcfm2acf --fai ../data/Camarosa_CMN_genomes.fasta.fai ../DoB_rand_samples_CallVariants.vcfUnfortunately, there was an error
SimpleVCF: unable to determine genotype for field=#0/0/0/0/0/0/0/0# at position: Fvb1-1:7753
The vcf file I used is made from callvariants, which is a script in bbmap.
Besides, I tried to get acf file from bam formate. I also failed with the following report.
./glactools bam2acf ../data/Camarosa_CMN_genomes.fasta ../virg_NA-UT-2-6-3.realigned.bam virg_NA-UT-2-6-3� � BC� 48m�UU�( 6����in�;.R
H(bwwk}9�yg;�k̹r>U)RZEv�D|Z4ټeҪyTkޱyݛ7Vn;uغ{6ͻh�uծ[fukҸ\frY廵nޡ]N[�J�s�5k5nZaZV**?ey3rZfgʫѦu
-ZTo:?b4�W/W!\�U 4W�ߨAFu+"\Fu+eggVdR1?Bn^6e&;+7'7��Ɏ%bżrrsfV_켊���+'B^V 7?3'r
K_/VN~n -3��r*V:lSBVvœd7'3?'䨜 m9Y_1#_ONǒ
AAg%LdṰX9Y9A97�ONFV^^n�bddeE[Hǻ�oٹsVQJŻuܣxN-�W%DW�e T
[E::bgzf_flush] File write failed (wrong size)
Write error
BAM2ACF: error writing header
May I have some help from anybody? Thanks!
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