wangyugui

Hi. Can we run one command to count/histo/stats without outputting the big mer_counts.jf file? For a 30x human wgs file, the mer_counts.jf file maybe 56G. We can use pipeline to...

Hi, big Peak memory of minimap2 in some case when WGS mapping . For some 1x WGS, the peak memory usage is about 15G, but for some 30x WGS, the...

bwa bwasw crashed with the error '[vfprintf(stdout)] Value too large for defined data type'

7

bwa bwasw crashed with the error '[vfprintf(stdout)] Value too large for defined data type'. Version: 0.7.15-r1142 I used 'bwa bwasw ' to compare two assembly reference. The contig size maybe...

a patch to fix some broken 'wbu' case

5

Hi, We still need "wbu" mode for pipe output, such as bwa | samtools fixmate | samtools sort but now 'samtools view -u ' is changed from 'wbu' to 'wb0',...

add support ploidy number over 2 to bcftools call?

3

Should we add support ploidy number over 2 to bcftools call? There are 4 or ploidy in some plant, so we need this feature.

Hi, '/usr/sbin/xfs_repair -n /dev/sdb2' triggered a core. ``` # gdb /usr/sbin/xfs_repair core.3466528 Reading symbols from /usr/sbin/xfs_repair...Reading symbols from .gnu_debugdata for /usr/sbin/xfs_repair...(no debugging symbols found)...done. (no debugging symbols found)...done. [New LWP...

Hi, '/usr/sbin/mkfs.xfs -dsu=65536 sw=1 /mnt/test/260.410113' triggered a core ``` # gdb /usr/sbin/mkfs.xfs core.410299 Reading symbols from /usr/sbin/mkfs.xfs...Reading symbols from .gnu_debugdata for /usr/sbin/mkfs.xfs...(no debugging symbols found)...done. (no debugging symbols found)...done. [New...

CPM(counts per M reads) for cuffdiff --max-bundle-frags will be better when different seq depth?

2

Hi. CPM(counts per M reads) for --max-bundle-frags will be better when different seq depth? When the total reads is 25M and --max-bundle-frags is 500K, then the CPM value will be...

segment when cufflinks with -mask-file

1

Hi. segment when cufflinks with -mask-file version:2.2.2 ``` (gdb) where #6 0x00007ff7680e0d4d in rewind () from /lib64/libc.so.6 #7 0x00000000005430be in read_transcripts (f=f@entry=0xd89770, seqdata=..., crc_result=..., keepAttrs=keepAttrs@entry=true) at gtf_tracking.cpp:595 #8 0x00000000004a14ab in...

reproduction problem of HaplotypeCaller when different interval split

3

Hi. The VCF output file of HaplotypeCaller is not same when different interval split. It seems that smaller region will product more var into vcf file. split1:chr unit 5,089,533 var...