hi all, i downloaded a bam file from 1000 genomes
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
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.