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Which is the best way to handle "Mate alignment does not match alignment start of mate" problem in r

nikkinathnikkinath GermanyMember

After running ValidateSamFile program on my bam files, I received following error message.

ERROR: Record 417172897, Read name J00137:36:H5TFGBBXX:6:1121:30675:9772, Mate alignment does not match alignment start of mate
ERROR: Record 472530216, Read name J00137:36:H5TFGBBXX:7:1105:26880:46451, Mate alignment does not match alignment start of mate
ERROR: Record 475397369, Read name J00137:34:H5LYHBBXX:1:1126:19806:37853, Mate alignment does not match alignment start of mate

for more than 100 records. How should I deal with this error message?

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