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Old 05-21-2013, 02:15 PM   #21
wangli
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Quote:
Originally Posted by Bruins View Post
Well... the problem is that after reading this thread and some googling, I get the feeling that SILENT (or IGNORE=) is the only solution, other than running FixMates.

That takes me back to my question one: what would be the consequence of using SILENT? Drio would you like to comment on that some more?

I'm planning to run some tests, I'll report back later.

Is anyone still interested in this question? I recently noticed the consequence of using the lenient stringency in Picard. When AddOrReplace read groups, the strict mode will generate some column like "RG:Z:***" in the reads, while the lenient mode will not, although both modes will generate bam files with @RG in the head. This will cause a further problem when calling SNPs in GATK, which just assume that you did not add read groups, while reading groups is required by GATK.

I spotted the problem, but havenot figured out how to solve it. Could anyone help me here?
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Old 07-09-2013, 07:05 PM   #22
ymc
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I am having this problem now with sam created by bwa-0.6.2

java -Xmx5g -jar ../picard/picard-tools-1.39/SortSam.jar I=P6T.sam SO=coordinate O=P6Tf.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true

Ignoring SAM validation error due to lenient parsing:
Error parsing text SAM file. MAPQ should be 0 for unmapped read.; Line 10820584
Ignoring SAM validation error due to lenient parsing:
Error parsing text SAM file. CIGAR should have zero elements for unmapped read.;

I am getting about 30 of these errors among my 39mil reads. Presumably because of the LENIENT flag, the program finishes with a decent sized bam. Is it ok?

Is this fixed in the bwa-0.7.5a and picard-1.94 combo??
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Old 07-09-2013, 09:17 PM   #23
ymc
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Interesting. With bwa-0.7.5a and picard-1.94 combo, CIGAR errors are gone but MAPQ errors remain.
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Old 09-23-2013, 05:31 AM   #24
vishnuamaram
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Hey guys,

Truly use VALIDATION_STRINGENCY=LENIENT OR SILENT. when u run most of the picard commands.

That will definitely help. I am experiencing it personally.

Good luck ahead to all NGS data analysing friends.

Regards,
Vishnu.
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Old 09-23-2013, 06:05 AM   #25
Naarkhoo
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Yes, it complains less ! but because we shut it down ; It does not necessarily solve the issue. So I would like to add, watch out the output when you are walking with VALIDATION_STRINGENCY=LENIENT OR SILENT
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