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hbeale/checkBamEOF_error

Created December 12, 2016 00:28
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check bam for EOF error
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checkBamEOF_error
for i in *.bam ; do echo -n $i; samtools view -h $i | head -1 ; done 2>&1 | grep '\['
# for malformed bams, the output is "EGAD00001001620_ICGC_MB110.sorted.bam[bam_header_read] EOF marker is
absent. The input is probably truncated."
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