Question: BWA-MEM alignment error with hg38 from GATK
0
gravatar for win
2.5 years ago by
win840
India
win840 wrote:

hi all, i downloaded a bam file from 1000 genomes

HG00100.chrom20.ILLUMINA.bwa.GBR.exome.20121211.bam

then i converted this to fastq using

sudo java -jar algorithms/picard/picard.jar SamToFastq VALIDATION_STRINGENCY=SILENT I=data/HG100.bam FASTQ=data/HG100.1.fastq SECOND_END_FASTQ=data/HG100.2.fastq UNPAIRED_FASTQ=data/HG100.unpaired.fastq

I have hg38 fasta and all associated indices from

https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

next i would like to align my fastq to hg38, the command i use is as follows

sudo ./algorithms/bwa-align/bwa mem -M references/hg38.fasta data/HG100.1.fastq data/HG100.2.fastq  > data/HG100.aligned.reads.sam

PROBLEM: i am getting a segmentation fault error when i use the hg38 from GATK HG38 bundle. HOWEVER, the above works fine when I use the hg38 from UCSC.

any ideas why i am unable to use the GATK version?

thanks in advance.

ngs • 1.3k views
ADD COMMENTlink written 2.5 years ago by win840
1
sudo ....

please , don't

ADD REPLYlink written 2.5 years ago by Pierre Lindenbaum129k

ok, wont. will change

ADD REPLYlink written 2.5 years ago by win840

what's the exact error message?

ADD REPLYlink written 2.5 years ago by Santosh Anand5.1k

core dumped. segmentation fault.

ADD REPLYlink written 2.5 years ago by win840
1

turns out the reference fasta file was corrupt for some reason.

ADD REPLYlink written 2.5 years ago by win840

Be aware it is recommended to shuffle the bam file previous to converting from bam to fastq.

ADD REPLYlink written 2.5 years ago by h.mon30k
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