ajc8

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ajc8
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  • I have solved the problem by changing the sample IDs. Thanks.
  • I just combined three samples (1 trio) that were missing and I noticed that the sample names were father, mother and proband, rather than their identifiers. I'm guessing this is the problem, that there are multiple samples with the same name being …
  • hi again, I have returned to phasing my trios and I'm still getting the same error message: This is what my ped file looks like: IA003 IA003C IA003D IA003M other CRMO And the vcf file I have just has the three members of the trio - with id…
  • Ok. I pulled out a family trio using vcftools. I'm still getting the same error message with just the family trio. I know for sure that the names in the vcf file match the names in the ped file.
  • I am getting the same error message - Sample lgsnd32563jz3 found in data sources but not in pedigree files with STRICT pedigree validation. However, the sample is in the pedigree file. I tried adding the flag --pedigreeValidationType SILENT to see…
  • I just uploaded it. The filename is ajc8_GATK_help. I also unintentionally uploaded it to a file on the site - Breakendbug. Can you delete it for me? Sorry about that. Thanks again for all your help.
  • I made the snippet from the pre-aligned bam no problem. When I try to do it with the aligned bam, I get the same malformed read error message. Is it okay if I just send you the prealigned snippet? If not, what should I do? Here is the command an…
  • hi, Well I ran everything through again and I got the malformed bam error message again. Here is the command line:java -Xmx8g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -nct 4 -I /Volumes/Thunderbolt/IA_084/IA084C.realigned.bam -R /Volumes/Thund…
  • Yes, I will do that now. I have been troubleshooting with one of the files since my last post. I normally fix mates and mark duplicates in Picard after realigning around indels, but I switched the order - first Picard steps and then indel realignm…
  • update: it is happening during the indel realignment - this is the entry from the realigned bam: MDF869:samtools-0.1.18 Allison$ ./samtools view /Volumes/Passport/IA_084/IA084C.realigned.bam |grep HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824HWI-ST11…
  • Hi again, I had not installed the correct Java, but doing so did not make a difference. Here are the two fastq reads: @HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 1:N:0:AAACATCCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCC…
  • I have been using GATK 2.3. So I downloaded the latest version (2.7) and updated java. I'm still getting the error message: Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sting/gatk/CommandLineGATK …
  • Hi, Thanks for your help. I only got the raw fastq files from the company - could these errors be something in the raw data?
  • Also, I tried adding "-filterMBQ" to the command and got a different error: ERROR stack trace java.lang.ArrayIndexOutOfBoundsException: -5 at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158) at org.broadinstitute.…
  • Hello, I am running BQSR and I'm getting the following error message: ERROR MESSAGE: SAM/BAM file SAMFileReader{/Volumes/Passport/IA_084/IA084C.realigned.fixed.dedup.bam} is malformed: BAM file has a read with mismatching number of bases and base q…