Wrong number of fields in PED files in PhaseByTransmission

huboqiang

Hello,all

while using the walker PhaseByTransmission I always get this error:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.1-12-ga99c19d): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: File associated with name java.io.FileReader@5cf7c5b5 is malformed: Bad PED line 1: wrong number of fields
##### ERROR ------------------------------------------------------------------------------------------

my conmmand is :

java -jar GenomeAnalysisTK-2.1-12-ga99c19d/GenomeAnalysisTK.jar -T  PhaseByTransmission -R GRCh37.fasta -V trios_457.chr22.vcf -ped trios_457.chr22.ped -pedValidationType SILENT -o o1.vcf

and my ped file is like this:

fam1    s_4     0       0       1       1       C       C       C       C       G       G
fam1    s_5     0       0       2       2       T       T       T       T       G       G
fam1    s_7     s_4     s_5     2       2       C       T       C       T       G       G

I do counted my vcf ped and map files and the result is:

-bash-4.1$ head -1 trios_457.chr22.ped |wc -w
1892         #( 6 columns for info + 943*2 columns for alleles )
-bash-4.1$ wc -l trios_457.chr22.map 
943 
-bash-4.1$ grep -v "#" trios_457.chr22.vcf | wc -l
943

My question is what's wrong with my my PED line?

Geraldine_VdAuwera

For your first error, you say you changed some of the columns after generating the file? That may have broken something. I would recommend generating the ped file again and trying again without making any manual modifications.

The second error is something else, it is complaining that your bam file does not have read groups. You will have to add read groups (with Picard tools) in order to proceed.

huboqiang

Thank you, Geraldine! I've solved the problem. For the first question, I checked the source code in Github and found it is because this PED file is not the PED file in PLINK. It contains only the first 6 columns in a PLINK format PED file, and no alleles, like a FAM file in PLINK. So I suggest the team to make that clear in the work-flows

For my second question, that's because of the mismatch of @RGs in my BAM header and my RG tags in the records. Thanks for your help!

huboqiang

Besides, I created my ped file by using vcftools

vcftools --vcf trios_457.chr22.vcf --plink --out trios_457.chr22.ped

I changed some columns so the PED file like this:

fam1 s_4 0 0 1 1 C C C C G G ……

fam1 s_5 0 0 2 2 T T T T G G .......

fam1 s_7 s_4 s_5 2 2 C T C T G G ......

Geraldine_VdAuwera

Hi there, could you please try again with the latest version of GATK? This may be a bug that was fixed since 2.1.

huboqiang

Oh I tried again with 2.3-5, and the error message is the same. Is there anything wrong with my PED file and can I generate that using vcftools?

huboqiang

In addition Geraldine, I met with another problem using ReadBackedPhasing. Did it mean that there are some problems in my vcf file?

java -jar GenomeAnalysisTK-2.3-5-g49ed93c/GenomeAnalysisTK.jar -T ReadBackedPhasing -R GRCh37.fasta -I 457.sort.bam --variant trios_457.all.vcf -L trios_457.all.vcf -o RBPphased_all.vcf --phaseQualityThresh 20.0

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

java.lang.NoClassDefFoundError: com/sun/javadoc/ProgramElementDoc at org.broadinstitute.sting.utils.exceptions.UserException$ReadMissingReadGroup.(UserException.java:281) at org.broadinstitute.sting.gatk.filters.MalformedReadFilter.checkHasReadGroup(MalformedReadFilter.java:63) at org.broadinstitute.sting.gatk.filters.MalformedReadFilter.filterOut(MalformedReadFilter.java:53) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.getNextRecord(CountingFilteringIterator.java:110) at org.broadinstitute.sting.gatk.filters.CountingFilteringIterator.(CountingFilteringIterator.java:58) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.applyDecoratingIterators(SAMDataSource.java:718) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.getIterator(SAMDataSource.java:633) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.getIterator(SAMDataSource.java:587) at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.seek(SAMDataSource.java:532) at org.broadinstitute.sting.gatk.executive.MicroScheduler.getReadIterator(MicroScheduler.java:315) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:70) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91) Caused by: java.lang.ClassNotFoundException: com.sun.javadoc.ProgramElementDoc at java.net.URLClassLoader$1.run(URLClassLoader.java:366) at java.net.URLClassLoader$1.run(URLClassLoader.java:355) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:354) at java.lang.ClassLoader.loadClass(ClassLoader.java:423) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) at java.lang.ClassLoader.loadClass(ClassLoader.java:356) ... 16 more

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 2.3-5-g49ed93c):

ERROR

ERROR Please visit the wiki to see if this is a known problem

ERROR If not, please post the error, with stack trace, to the GATK forum

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions http://www.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: com/sun/javadoc/ProgramElementDoc

ERROR ------------------------------------------------------------------------------------------

Thanks!

Geraldine_VdAuwera

Thanks for reporting your solution; I'll update the documentation accordingly.