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GATK flagstats show 0.0 % properly paired reads


Hi everyone,

I used GATK Flagstats walker. I am getting 0.0% properly paired reads in the BAM file. I sorted my BAM file and marked the duplicates as well. is there any BAM FLAG is missing in my file or mapping results are bad quality. Note that my average mapping quality (MAPQ) is more than 30.. and average read legth is 150 bp. i used bwa-mem for mapping to reference genome. and processed my data with picard-tools before using in GATK.

can you please help help me tracking this issue?

my GATK arguments were:
java -Xmx15g -jar /GTK/GenomeAnalysisTK.jar -T FlagStat \
-log Flagstat.log \
-R /Ref/human_g1k_v37.fasta \
-I /CHG000691/Dedup_Sort_CHG000691_PE.bam \
-o /CHG000691/Dedup_Sort_CHG000691_flagstat.txt

606634523 in total
0 QC failure
24671783 duplicates
599254096 mapped (98.78%)
606634523 paired in sequencing
303086535 read1
303547988 read2
0 properly paired (0.00%)
593494816 with itself and mate mapped
5759280 singletons (0.95%)
28638158 with mate mapped to a different chr
9047446 with mate mapped to a different chr (mapQ>=5)

Thank you very much!


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